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Why is HRun annotation not displayed in vcf (GATK version 2.5.2)?

Why is HRun annotation not displayed in vcf (GATK version 2.5.2)?

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Do you mean that the annotation is missing from all sites, or only from some? Keep in mind that this annotation can only be computed for bi-allelic sites.

  • Shrey_SShrey_S Member

    It's missing from all biallelic sites. Also it's definition is missing from the header of vcf

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I see -- can you please post the command-line you used to generate the VCF?

  • Shrey_SShrey_S Member

    java -Xmx2G -jar /home/bdaber01/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R genomes/hg19_genome.fa -T UnifiedGenotyper -I Sample.bam --dbsnp hg19_dbsnp137.vcf -o Sample.GATK.vcf -nt 4 -glm BOTH -mbq 15 -dt NONE -minIndelCnt 3 -minIndelFrac 0.04 -nda -stand_emit_conf 10.0 -L region.BED

  • pdexheimerpdexheimer Member ✭✭✭✭

    Isn't this expected? The release notes from v2.0 say "The new TandemRepeatAnnotator is now a standard annotation while HRun has been retired"

  • Shrey_SShrey_S Member

    Oh I see..Sorry I missed that statement.
    But I am not able to see the RPA annotations for any of the variants in my vcf. I am comparing the 1.6 version GATK with 2.5 and those variants which had HRun=12 or 11 in the old vcf don't have RPA annotations now in the new vcf.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @Shrey_S,

    If you don't specify any annotations in your command-line, only the defaults will be annotated. Defaults may change between versions, and have certainly changed between 1.6 and 2.5.

    If you want to add annotations that are missing, you can use VariantAnnotator to do so.

  • Shrey_SShrey_S Member

    RPA is still not getting annotated.
    See below:

    INFO 10:26:01,535 ArgumentTypeDescriptor - Dynamically determined type of Sample.GATK.vcf to be VCF
    INFO 10:26:01,565 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:26:01,565 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
    INFO 10:26:01,565 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 10:26:01,566 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 10:26:01,569 HelpFormatter - Program Args: -T VariantAnnotator -I Sample.bam -o Sample.GATK.VA.vcf -A TandemRepeatAnnotator --variant Sample.GATK.vcf -L Sample.GATK.vcf --dbsnp dbsnp/hg19_dbsnp137.vcf -R genomes/hg19_genome.fa
    INFO 10:26:01,569 HelpFormatter - Date/Time: 2013/06/11 10:26:01
    INFO 10:26:01,569 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:26:01,569 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:26:01,582 ArgumentTypeDescriptor - Dynamically determined type of Sample.GATK.vcf to be VCF
    INFO 10:26:01,591 ArgumentTypeDescriptor - Dynamically determined type of dbsnp/hg19_dbsnp137.vcf to be VCF
    INFO 10:26:01,642 GenomeAnalysisEngine - Strictness is SILENT
    INFO 10:26:01,875 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 10:26:01,883 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 10:26:01,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
    INFO 10:26:01,934 RMDTrackBuilder - Loading Tribble index from disk for file Sample.GATK.vcf
    INFO 10:26:01,982 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp/hg19_dbsnp137.vcf
    INFO 10:26:02,169 IntervalUtils - Processing 36 bp from intervals
    INFO 10:26:02,241 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files
    INFO 10:26:02,295 GenomeAnalysisEngine - Done creating shard strategy
    INFO 10:26:02,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 10:26:02,296 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
    INFO 10:26:05,303 VariantAnnotator - Processed 33 loci.

    INFO 10:26:06,043 ProgressMeter - done 4.40e+01 3.0 s 23.6 h 97.2% 3.0 s 0.0 s
    INFO 10:26:06,044 ProgressMeter - Total runtime 3.75 secs, 0.06 min, 0.00 hours
    INFO 10:26:06,044 MicroScheduler - 7 reads were filtered out during traversal out of 191449 total (0.00%)
    INFO 10:26:06,045 MicroScheduler - -> 7 reads (0.00% of total) failing UnmappedReadFilter

    and the variant output is:

    chr2 209113192 rs11554137 G A 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-32.776;DB;DP=13155;Dels=0.00;FS=1.389;HaplotypeScore=1481.1207;MLEAC=1;MLEAF=0.500;MQ=69.97;MQ0=0;MQRankSum=0.085;NDA=1;QD=2
    .49;ReadPosRankSum=3.631 GT:AD:DP:GQ:PL 0/1:6173,6924:12488:99:32767,0,32767
    chr2 212578391 . AAA A 32729.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.735;DP=3630;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=69.98;MQ0=0;MQRankSum=-0.262;NDA=3;QD=4.51;ReadPosRankSum=1.976 GT:AD:DP:GQ:PL 0/1:0
    ,44:3630:99:10040,0,32767

    chr2 212578392 . AA A 32729.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=6.917;DP=3630;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=69.98;MQ0=0;MQRankSum=-0.260;NDA=3;QD=9.02;ReadPosRankSum=7.783 GT:AD:DP:GQ:PL 0/1:0
    ,120:3630:99:16526,0,32310

    chr3 178921639 rs2699895 C A 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DB;DP=5390;Dels=0.00;FS=0.096;HaplotypeScore=583.9668;MLEAC=1;MLEAF=0.500;MQ=69.97;MQ0=0;MQRankSum=1.081;NDA=1;QD=6.07;
    ReadPosRankSum=2.177 GT:AD:DP:GQ:PL 0/1:2697,2669:5366:99:32767,0,32767
    chr4 1806163 . G C 3964.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.128;DP=1430;Dels=0.00;FS=0.228;HaplotypeScore=115.9714;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=1.050;NDA=1;QD=2.77;ReadPosRankSum=-0.961 GT:AD
    :DP:GQ:PL 0/1:1117,309:1359:99:3993,0,23041
    chr4 1807894 rs7688609 G A 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.110;DB;DP=2356;Dels=0.00;FS=0.000;HaplotypeScore=299.6634;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;MQRankSum=-0.482;NDA=1;QD=13.90;ReadPosR
    ankSum=0.480 GT:AD:DP:GQ:PL 1/1:6,2346:2347:99:32767,3687,0
    chr4 55141055 rs1873778 A G 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.327;DB;DP=5754;Dels=0.00;FS=0.000;HaplotypeScore=430.6727;MLEAC=2;MLEAF=1.00;MQ=69.96;MQ0=0;MQRankSum=-0.643;NDA=1;QD=5.69;
    ReadPosRankSum=0.949 GT:AD:DP:GQ:PL 1/1:20,5724:5724:99:32767,8669,0
    chr4 55152040 rs2228230 C T 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.713;DB;DP=10007;Dels=0.00;FS=0.676;HaplotypeScore=586.2213;MLEAC=1;MLEAF=0.500;MQ=69.81;MQ0=0;MQRankSum=-1.668;NDA=1;QD=3.
    27;ReadPosRankSum=1.542 GT:AD:DP:GQ:PL 0/1:4324,5667:9507:99:32767,0,32767
    chr4 55599436 rs1008658 T C 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.526;DB;DP=7477;Dels=0.00;FS=0.000;HaplotypeScore=700.5357;MLEAC=2;MLEAF=1.00;MQ=69.70;MQ0=0;MQRankSum=0.348;NDA=1;QD=4.38;Re
    adPosRankSum=0.023 GT:AD:DP:GQ:PL 1/1:19,7454:7454:99:32767,11661,0
    chr4 55946081 rs4421048 A G 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.022;DB;DP=5180;Dels=0.00;FS=0.000;HaplotypeScore=420.9868;MLEAC=2;MLEAF=1.00;MQ=69.97;MQ0=0;MQRankSum=-0.164;NDA=1;QD=6.32;R
    eadPosRankSum=0.462 GT:AD:DP:GQ:PL 1/1:6,5158:5164:99:32767,7811,0
    chr4 55962559 rs202176656 A AG 32729.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.540;DB;DP=8464;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=69.94;MQ0=0;MQRankSum=0.251;NDA=2;QD=3.87;ReadPosRankSum=0.088 GT:AD:DP:GQ:P
    L 0/1:4304,3712:8464:99:32767,0,32767
    chr5 112175711 rs139387758 G A 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-18.172;DB;DP=6139;Dels=0.00;FS=0.564;HaplotypeScore=614.2586;MLEAC=1;MLEAF=0.500;MQ=69.80;MQ0=0;MQRankSum=0.055;NDA=1;QD=5.3
    3;ReadPosRankSum=1.117 GT:AD:DP:GQ:PL 0/1:3135,3002:5984:99:32767,0,32767
    chr5 112175770 rs41115 G A 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.458;DB;DP=12393;Dels=0.00;FS=0.000;HaplotypeScore=518.7192;MLEAC=2;MLEAF=1.00;MQ=69.66;MQ0=0;MQRankSum=-1.252;NDA=1;QD=2.64;ReadPosR
    ankSum=2.424 GT:AD:DP:GQ:PL 1/1:44,12252:12271:99:32767,18735,0
    chr7 55248930 rs41323247 C T 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-7.444;DB;DP=4564;Dels=0.00;FS=0.211;HaplotypeScore=384.0062;MLEAC=1;MLEAF=0.500;MQ=69.99;MQ0=0;MQRankSum=-1.016;NDA=1;QD=7.1
    7;ReadPosRankSum=18.686 GT:AD:DP:GQ:PL 0/1:2152,2407:4335:99:32767,0,32767
    chr7 55249063 rs1050171 G A 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.130;DB;DP=6414;Dels=0.00;FS=0.000;HaplotypeScore=555.7712;MLEAC=1;MLEAF=0.500;MQ=69.98;MQ0=0;MQRankSum=-0.829;NDA=1;QD=5.1
    0;ReadPosRankSum=25.102 GT:AD:DP:GQ:PL 0/1:3044,3364:6094:99:32767,0,32767
    chr7 116340269 rs28444388 C T 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.829;DB;DP=6426;Dels=0.00;FS=0.852;HaplotypeScore=571.6218;MLEAC=1;MLEAF=0.500;MQ=69.74;MQ0=0;MQRankSum=-1.728;NDA=1;QD=5.09
    ;ReadPosRankSum=0.173 GT:AD:DP:GQ:PL 0/1:3394,3024:6103:99:32767,0,32767
    chr7 128846469 rs2735842 A G 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.577;DB;DP=1676;Dels=0.00;FS=0.000;HaplotypeScore=137.6290;MLEAC=2;MLEAF=1.00;MQ=69.99;MQ0=0;MQRankSum=-1.194;NDA=1;QD=19.53
    ;ReadPosRankSum=0.386 GT:AD:DP:GQ:PL 1/1:2,1672:1672:99:32767,2549,0
    chr9 80343598 . AAAA A 23908.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=10.336;DP=9964;FS=2.848;MLEAC=1;MLEAF=0.500;MQ=69.99;MQ0=0;MQRankSum=-1.347;NDA=1;QD=0.80;ReadPosRankSum=-60.205 GT:AD:DP:GQ:P
    L 0/1:7133,2324:9964:99:23946,0,32767

    chr9 80343599 . AAA A 32729.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.724;DP=9964;FS=6.772;MLEAC=1;MLEAF=0.500;MQ=69.99;MQ0=0;MQRankSum=-0.317;NDA=1;QD=1.64;ReadPosRankSum=-57.716 GT:AD:DP:GQ:P
    L 0/1:2949,2922:9963:99:32767,0,32767

    chr9 80343600 . AA A 32729.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=6.420;DP=9964;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=69.99;MQ0=0;MQRankSum=-1.435;NDA=3;QD=3.28;ReadPosRankSum=-11.916 GT:AD:DP:GQ:PL 0/1:0
    ,78:9964:99:32767,0,32767

    chr9 133747536 rs141920514 A G 14712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.247;DB;DP=1438;Dels=0.00;FS=0.000;HaplotypeScore=97.4397;MLEAC=1;MLEAF=0.500;MQ=69.98;MQ0=0;MQRankSum=1.010;NDA=1;QD=10.23
    ;ReadPosRankSum=10.668 GT:AD:DP:GQ:PL 0/1:657,781:1367:99:14741,0,12534
    chr9 133748202 rs34842572 T C 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.749;DB;DP=6068;Dels=0.00;FS=0.000;HaplotypeScore=600.1826;MLEAC=1;MLEAF=0.500;MQ=69.39;MQ0=0;MQRankSum=-3.236;NDA=1;QD=5.40
    ;ReadPosRankSum=0.203 GT:AD:DP:GQ:PL 0/1:2277,3783:5765:99:32767,0,32767
    chr10 43613843 . G T 32738.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.940;DP=2250;Dels=0.00;FS=0.000;HaplotypeScore=164.9970;MLEAC=2;MLEAF=1.00;MQ=69.06;MQ0=0;MQRankSum=-2.176;NDA=1;QD=14.55;ReadPosRank
    Sum=1.271 GT:AD:DP:GQ:PL 1/1:3,2233:2236:99:32767,3477,0
    chr11 108117906 . TT T 645.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.299;DP=12298;FS=1.605;MLEAC=1;MLEAF=0.500;MQ=69.96;MQ0=0;MQRankSum=-2.639;NDA=3;QD=0.05;ReadPosRankSum=-41.092 GT:AD:DP:GQ:PL 0/1:1
    0820,672:12297:99:683,0,32767

    chr11 108218196 . T C 21147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.212;DP=1932;Dels=0.00;FS=0.000;HaplotypeScore=169.6556;MLEAC=1;MLEAF=0.500;MQ=69.97;MQ0=0;MQRankSum=-0.158;NDA=1;QD=10.95;ReadPosR
    ankSum=1.130 GT:AD:DP:GQ:PL 0/1:828,1102:1836:99:21176,0,15606
    chr11 108225661 . A G 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.135;DP=6980;Dels=0.00;FS=0.000;HaplotypeScore=611.5917;MLEAC=1;MLEAF=0.500;MQ=69.99;MQ0=0;MQRankSum=-1.623;NDA=1;QD=4.69;ReadPosRan
    kSum=3.504 GT:AD:DP:GQ:PL 0/1:3882,3088:6631:99:32767,0,32767
    chr17 7577084 . T C 2703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=7.333;DP=2964;Dels=0.00;FS=0.190;HaplotypeScore=326.5445;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=-0.483;NDA=1;QD=0.91;ReadPosRankSum=7.216 GT:AD
    :DP:GQ:PL 0/1:2563,398:2813:99:2732,0,32767
    chr17 7577547 . C A 18419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.351;DP=4933;Dels=0.00;FS=0.605;HaplotypeScore=421.9916;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=0.729;NDA=1;QD=3.73;ReadPosRankSum=0.4
    01 GT:AD:DP:GQ:PL 0/1:3657,1253:4687:99:18448,0,32767
    chr17 7578115 . T C 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.694;DP=4730;Dels=0.00;FS=0.000;HaplotypeScore=374.2892;MLEAC=1;MLEAF=0.500;MQ=69.96;MQ0=0;MQRankSum=0.478;NDA=1;QD=6.92;ReadPosRankSum=5.28
    4 GT:AD:DP:GQ:PL 0/1:2239,2479:4492:99:32767,0,32767
    chr19 1221293 . C T 19278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=2977;Dels=0.00;FS=0.277;HaplotypeScore=256.9163;MLEAC=1;MLEAF=0.500;MQ=69.97;MQ0=0;MQRankSum=0.287;NDA=1;QD=6.48;ReadPosRankSum=0.67
    2 GT:AD:DP:GQ:PL 0/1:1902,1068:2829:99:19307,0,32767
    chr19 3119239 . C T 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.965;DP=3651;Dels=0.00;FS=0.754;HaplotypeScore=290.1067;MLEAC=1;MLEAF=0.500;MQ=69.86;MQ0=0;MQRankSum=-0.896;NDA=1;QD=8.97;ReadPosRankSum=1.0
    69 GT:AD:DP:GQ:PL 0/1:1543,2098:3463:99:32767,0,28774
    chr19 17945781 . G A 32738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.279;DP=3576;Dels=0.00;FS=0.122;HaplotypeScore=355.1640;MLEAC=1;MLEAF=0.500;MQ=69.98;MQ0=0;MQRankSum=0.364;NDA=1;QD=9.16;ReadPosRank
    Sum=-2.993 GT:AD:DP:GQ:PL 0/1:1319,2253:3397:99:32767,0,23983
    chr22 24145675 . G C 32738.77 . AC=2;AF=1.00;AN=2;DP=3667;Dels=0.00;FS=0.000;HaplotypeScore=398.6356;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;NDA=1;QD=8.93 GT:AD:DP:GQ:PL 1/1:0,3645:3645:99:32767,5505
    ,0

    With GATK 1.6 version the above variants were having the HRun Annotation ( as standard annotation) as seen below:

    chr2 209113192 rs11554137 G A 134072.27 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-33.319;DB;DP=13155;Dels=0.00;FS=9.204;HRun=0;HaplotypeScore=1481.1207;MQ=69.97;MQ0=0;MQRankSum=-0.183;NDA=1;QD=10.19;ReadPosRankSum=6.599;SB=-99558.04 GT:AD:DP:GQ:PL 0/1:6173,6924:13145:99:134072,0,116512
    chr2 212578391 . AAA A 10040.92 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=2.641;DP=3630;FS=11.663;HRun=11;HaplotypeScore=14441.6325;MQ=69.98;MQ0=0;MQRankSum=1.365;NDA=5;QD=2.77;ReadPosRankSum=0.175;SB=-4925.60 GT:AD:DP:GQ:PL 0/1:3269,350:3630:99:10041,0,56225
    chr2 212578392 . AA A 16526.88 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=3.424;DP=3630;FS=8.778;HRun=12;HaplotypeScore=13515.1306;MQ=69.98;MQ0=0;MQRankSum=-0.276;NDA=6;QD=4.55;ReadPosRankSum=-6.731;SB=-7839.87 GT:AD:DP:GQ:PL 0/1:2816,800:3630:99:16527,0,32309

    chr3 178921639 rs2699895 C A 51620.89 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=1.026;DB;DP=5390;Dels=0.00;FS=0.718;HRun=1;HaplotypeScore=583.9668;MQ=69.97;MQ0=0;MQRankSum=0.383;NDA=1;QD=9.58;ReadPosRankSum=2.481;SB=-44962.31 GT:AD:DP:GQ:PL 0/1:2697,2669:5382:99:51621,0,52110
    chr4 1806163 . G C 4748.33 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=1.195;DP=1430;Dels=0.00;FS=1.279;HRun=1;HaplotypeScore=115.9714;MQ=70.00;MQ0=0;MQRankSum=-1.150;NDA=1;QD=3.32;ReadPosRankSum=7.142;SB=-3570.14 GT:AD:DP:GQ:PL 0/1:1117,309:1430:99:4748,0,23005
    chr4 1807894 rs7688609 G A 53670.09 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.995;DB;DP=2356;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=299.6634;MQ=70.00;MQ0=0;MQRankSum=0.100;NDA=1;QD=22.78;ReadPosRankSum=0.610;SB=-32163.47 GT:AD:DP:GQ:PL 1/1:6,2346:2355:99:53670,3570,0
    chr4 55141055 rs1873778 A G 127817.09 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.120;DB;DP=5754;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=430.6727;MQ=69.96;MQ0=0;MQRankSum=0.794;NDA=1;QD=22.21;ReadPosRankSum=0.801;SB=-111668.96 GT:AD:DP:GQ:PL 1/1:20,5724:5749:99:127817,8293,0
    chr4 55152040 rs2228230 C T 111430.89 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-6.197;DB;DP=10007;Dels=0.00;FS=4.723;HRun=1;HaplotypeScore=586.2213;MQ=69.81;MQ0=0;MQRankSum=-0.440;NDA=1;QD=11.14;ReadPosRankSum=-0.673;SB=-86588.32 GT:AD:DP:GQ:PL 0/1:4324,5667:10007:99:111431,0,82037
    chr4 55599436 rs1008658 T C 170383.50 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.973;DB;DP=7477;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=700.5357;MQ=69.70;MQ0=0;MQRankSum=-0.214;NDA=1;QD=22.79;ReadPosRankSum=-0.386;SB=-141352.22 GT:AD:DP:GQ:PL 1/1:19,7454:7477:99:170383,11308,0
    chr4 55946081 rs4421048 A G 115275.28 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-0.485;DB;DP=5180;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=420.9868;MQ=69.97;MQ0=0;MQRankSum=0.529;NDA=1;QD=22.25;ReadPosRankSum=-0.293;SB=-102315.71 GT:AD:DP:GQ:PL 1/1:6,5158:5178:99:115275,7686,0
    chr4 55962559 rs202176656 A AG 143311.43 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=0.487;DB;DP=8464;FS=0.396;HRun=0;HaplotypeScore=17329.2348;MQ=69.94;MQ0=0;MQRankSum=0.811;NDA=2;QD=16.93;ReadPosRankSum=4.227;SB=-70741.64 GT:AD:DP:GQ:PL 0/1:4744,3697:8464:99:143311,0,188153
    chr5 112175711 rs139387758 G A 57752.78 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-17.377;DB;DP=6139;Dels=0.00;FS=0.773;HRun=0;HaplotypeScore=614.2586;MQ=69.80;MQ0=0;MQRankSum=-0.616;NDA=1;QD=9.41;ReadPosRankSum=0.521;SB=-49087.95 GT:AD:DP:GQ:PL 0/1:3135,3002:6138:99:57753,0,61045
    chr5 112175770 rs41115 G A 275996.56 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.493;DB;DP=12393;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=518.7192;MQ=69.66;MQ0=0;MQRankSum=0.247;NDA=1;QD=22.27;ReadPosRankSum=0.881;SB=-242303.02 GT:AD:DP:GQ:PL 1/1:44,12252:12367:99:275997,17840,0
    chr7 55248930 rs41323247 C T 47227.69 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-6.730;DB;DP=4564;Dels=0.00;FS=7.178;HRun=0;HaplotypeScore=384.0062;MQ=69.99;MQ0=0;MQRankSum=-0.031;NDA=1;QD=10.35;ReadPosRankSum=7.245;SB=-31021.37 GT:AD:DP:GQ:PL 0/1:2152,2407:4563:99:47228,0,41822
    chr7 55249063 rs1050171 G A 65918.29 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-3.657;DB;DP=6414;Dels=0.00;FS=0.559;HRun=1;HaplotypeScore=555.7712;MQ=69.98;MQ0=0;MQRankSum=-0.644;NDA=1;QD=10.28;ReadPosRankSum=1.296;SB=-56360.26 GT:AD:DP:GQ:PL 0/1:3044,3364:6414:99:65918,0,57821
    chr7 116340269 rs28444388 C T 58219.48 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=0.440;DB;DP=6426;Dels=0.00;FS=2.124;HRun=1;HaplotypeScore=571.6218;MQ=69.74;MQ0=0;MQRankSum=14.976;NDA=1;QD=9.06;ReadPosRankSum=-1.507;SB=-46939.00 GT:AD:DP:GQ:PL 0/1:3394,3024:6424:99:58219,0,66174
    chr7 128846469 rs2735842 A G 37269.08 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-0.724;DB;DP=1676;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=137.6290;MQ=69.99;MQ0=0;MQRankSum=0.179;NDA=1;QD=22.24;ReadPosRankSum=-1.202;SB=-31818.72 GT:AD:DP:GQ:PL 1/1:2,1672:1675:99:37269,2508,0
    chr9 80343598 . AAAA A 23950.57 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=11.267;DP=9964;FS=4.137;HRun=10;HaplotypeScore=41966.6897;MQ=69.99;MQ0=0;MQRankSum=1.064;NDA=3;QD=2.40;ReadPosRankSum=-68.497;SB=-11530.84 GT:AD:DP:GQ:PL 0/1:9500,462:9964:99:23951,0,142187
    chr9 80343599 . AAA A 73269.32 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-2.549;DP=9964;FS=6.552;HRun=11;HaplotypeScore=37909.3922;MQ=69.99;MQ0=0;MQRankSum=0.549;NDA=4;QD=7.35;ReadPosRankSum=-62.449;SB=-36401.14 GT:AD:DP:GQ:PL 0/1:7999,1959:9963:99:73269,0,78464
    chr9 80343600 . AA A 102561.40 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=5.033;DP=9964;FS=4.563;HRun=12;HaplotypeScore=33904.7292;MQ=69.99;MQ0=0;MQRankSum=-1.745;NDA=6;QD=10.29;ReadPosRankSum=-70.238;SB=-51066.27 GT:AD:DP:GQ:PL 0/1:5962,3990:9964:99:102561,0,34467

    chr9 133747536 rs141920514 A G 15381.37 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-4.529;DB;DP=1438;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=97.4397;MQ=69.98;MQ0=0;MQRankSum=0.251;NDA=1;QD=10.70;ReadPosRankSum=9.575;SB=-12561.84 GT:AD:DP:GQ:PL 0/1:657,781:1438:99:15381,0,12512
    chr9 133748202 rs34842572 T C 74879.56 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=6.026;DB;DP=6068;Dels=0.00;FS=0.920;HRun=0;HaplotypeScore=600.1826;MQ=69.39;MQ0=0;MQRankSum=-3.848;NDA=1;QD=12.34;ReadPosRankSum=-3.134;SB=-63322.08 GT:AD:DP:GQ:PL 0/1:2277,3783:6068:99:74880,0,41605
    chr10 43613843 . G T 50840.35 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=2.927;DP=2250;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=164.9970;MQ=69.06;MQ0=0;MQRankSum=0.685;NDA=1;QD=22.60;ReadPosRankSum=1.185;SB=-33749.81 GT:AD:DP:GQ:PL 1/1:3,2233:2250:99:50840,3477,0
    chr11 108117906 . TT T 644.05 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=0.421;DP=12298;FS=0.523;HRun=8;HaplotypeScore=27632.0151;MQ=69.96;MQ0=0;MQRankSum=0.362;NDA=5;QD=0.05;ReadPosRankSum=-51.661;SB=-204.79 GT:AD:DP:GQ:PL 0/1:11139,1141:12297:99:683,0,258357
    chr11 108218196 . T C 21694.14 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-2.623;DP=1932;Dels=0.00;FS=0.163;HRun=0;HaplotypeScore=169.6556;MQ=69.97;MQ0=0;MQRankSum=-0.237;NDA=1;QD=11.23;ReadPosRankSum=1.378;SB=-18948.56 GT:AD:DP:GQ:PL 0/1:828,1102:1932:99:21694,0,15594
    chr11 108225661 . A G 58639.63 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=2.974;DP=6980;Dels=0.00;FS=0.535;HRun=0;HaplotypeScore=611.5917;MQ=69.99;MQ0=0;MQRankSum=-0.080;NDA=1;QD=8.40;ReadPosRankSum=2.272;SB=-50750.68 GT:AD:DP:GQ:PL 0/1:3882,3088:6980:99:58640,0,76382
    chr17 7577084 . T C 4440.59 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=7.188;DP=2964;Dels=0.00;FS=0.604;HRun=2;HaplotypeScore=326.5445;MQ=70.00;MQ0=0;MQRankSum=-1.016;NDA=1;QD=1.50;ReadPosRankSum=-0.171;SB=-3426.65 GT:AD:DP:GQ:PL 0/1:2563,398:2961:99:4441,0,52832
    chr17 7577547 . C A 20619.47 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-2.900;DP=4933;Dels=0.00;FS=1.603;HRun=0;HaplotypeScore=421.9916;MQ=70.00;MQ0=0;MQRankSum=0.430;NDA=1;QD=4.18;ReadPosRankSum=0.790;SB=-15456.29 GT:AD:DP:GQ:PL 0/1:3657,1253:4933:99:20619,0,74545
    chr17 7578115 . T C 48814.09 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=4.156;DP=4730;Dels=0.00;FS=2.260;HRun=2;HaplotypeScore=374.2892;MQ=69.96;MQ0=0;MQRankSum=0.003;NDA=1;QD=10.32;ReadPosRankSum=1.583;SB=-38843.49 GT:AD:DP:GQ:PL 0/1:2239,2479:4728:99:48814,0,43040
    chr19 1221293 . C T 19273.41 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=1.052;DP=2977;Dels=0.00;FS=1.385;HRun=0;HaplotypeScore=256.9163;MQ=69.97;MQ0=0;MQRankSum=1.251;NDA=1;QD=6.47;ReadPosRankSum=0.155;SB=-16344.39 GT:AD:DP:GQ:PL 0/1:1902,1068:2977:99:19273,0,37899
    chr19 3119239 . C T 41249.89 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=2.191;DP=3651;Dels=0.00;FS=1.496;HRun=0;HaplotypeScore=290.1067;MQ=69.86;MQ0=0;MQRankSum=-0.796;NDA=1;QD=11.30;ReadPosRankSum=2.415;SB=-35041.48 GT:AD:DP:GQ:PL 0/1:1543,2098:3645:99:41250,0,28735
    chr19 17945781 . G A 44870.10 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=2.834;DP=3576;Dels=0.00;FS=0.792;HRun=0;HaplotypeScore=355.1640;MQ=69.98;MQ0=0;MQRankSum=0.804;NDA=1;QD=12.55;ReadPosRankSum=2.339;SB=-38646.75 GT:AD:DP:GQ:PL 0/1:1319,2253:3575:99:44870,0,23947
    chr22 24145675 . G C 80886.21 PASS AC=2;AF=1.00;AN=2;DP=3667;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=398.6356;MQ=70.00;MQ0=0;NDA=1;QD=22.06;SB=-70019.07 GT:AD:DP:GQ:PL 1/1:0,3645:3662:99:80886,5505,0

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    As far as I can tell the tandem repeat annotation doesn't apply to any of these variants. In that case it will not get added at all. To make sure, can you please post the header of your VCF? All annotations that were successfully run should be written there.

    And as we've said, the HRun annotation is no longer applicable because we found that it was not working properly, so it's normal that you no longer see it in the new files.

  • Shrey_SShrey_S Member
    edited June 2013

    Header is right here:

    ##fileformat=VCFv4.1
    ##FILTER=<ID=LowQual,Description="Low quality">
    ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
    ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
    ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
    ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
    ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
    ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
    ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
    ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
    ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
    ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
    ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
    ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
    ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
    ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
    ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
    ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
    ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
    ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
    ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
    ##INFO=<ID=NDA,Number=1,Type=Integer,Description="Number of alternate alleles discovered (but not necessarily genotyped) at this site">
    ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
    **##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
    ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">**
    ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
    ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
    ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[Sample.bam] read_buffer_size
    =null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[Target.BED] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genomes/hg19_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=4
    0.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less
    _than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creatio
    n_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationTyp
    e=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=true pair_hmm_impl
    ementation=ORIGINAL min_base_quality_score=15 max_deletion_fraction=0.05 min_indel_count_for_genotyping=3 min_indel_fraction_per_sample=0.04 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ign
    oreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_thresh
    old_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=
    30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EX
    ACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name=dbsnp source=dbsnp/hg19_dbsnp137.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadin
    stitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotat
    ion=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
    ##VariantAnnotator="analysis_type=VariantAnnotator input_file=[Sample.bam] read_buffer_size=n
    ull phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[Sample.GATK.vcf] excludeIntervals=null i
    nterval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=genomes/hg19_genome.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=B
    Y_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=nul
    l quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT re
    move_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file
    _handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false variant=(R
    odBinding name=variant source=Sample.GATK.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding n
    ame=dbsnp source=dbsnp/hg19_dbsnp137.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sit
    es_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub annotation=[TandemRepeatAnnotator] excludeAnnotation=[] group=[] expression={} useAllAnnotations=
    false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
    ##contig=<ID=chr1,length=249250621,assembly=hg19>
    ##contig=<ID=chr2,length=243199373,assembly=hg19>
    ##contig=<ID=chr3,length=198022430,assembly=hg19>
    ##contig=<ID=chr4,length=191154276,assembly=hg19>
    ##contig=<ID=chr5,length=180915260,assembly=hg19>
    ##contig=<ID=chr6,length=171115067,assembly=hg19>
    ##contig=<ID=chr7,length=159138663,assembly=hg19>
    ##contig=<ID=chr8,length=146364022,assembly=hg19>
    ##contig=<ID=chr9,length=141213431,assembly=hg19>
    ##contig=<ID=chr10,length=135534747,assembly=hg19>
    ##contig=<ID=chr11,length=135006516,assembly=hg19>
    ##contig=<ID=chr12,length=133851895,assembly=hg19>
    ##contig=<ID=chr13,length=115169878,assembly=hg19>
    ##contig=<ID=chr14,length=107349540,assembly=hg19>
    ##contig=<ID=chr15,length=102531392,assembly=hg19>
    ##contig=<ID=chr16,length=90354753,assembly=hg19>
    ##contig=<ID=chr17,length=81195210,assembly=hg19>
    ##contig=<ID=chr18,length=78077248,assembly=hg19>
    ##contig=<ID=chr19,length=59128983,assembly=hg19>
    ##contig=<ID=chr20,length=63025520,assembly=hg19>
    ##contig=<ID=chr21,length=48129895,assembly=hg19>
    ##contig=<ID=chr22,length=51304566,assembly=hg19>
    ##contig=<ID=chrX,length=155270560,assembly=hg19>
    ##contig=<ID=chrY,length=59373566,assembly=hg19>
    ##contig=<ID=chrM,length=16571,assembly=hg19>
    ##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
    ##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
    ##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
    ##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
    ##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
    ##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
    ##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
    ##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
    ##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
    ##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
    ##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
    ##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
    ##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
    ##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
    ##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
    ##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
    ##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
    ##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
    ##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
    ##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
    ##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
    ##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
    ##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
    ##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
    ##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
    ##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
    ##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
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    ##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
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    ##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
    ##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
    ##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
    ##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
    ##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
    ##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
    ##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
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    ##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
    ##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
    ##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
    ##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
    ##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
    ##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
    ##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
    ##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
    ##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
    ##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
    ##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
    ##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
    ##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
    ##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
    ##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
    ##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
    ##reference=file:///Drive_D/Databases/genomes/hg19_genome.fa
    

    And ya I pasted the previous version's HRun annotations to let you know that the variants which were annotated with high HRun i.e. 10 or 12 before are not at all annotated with RPA now.
    So then whats the purpose of RPA? Isnt it meant to replace Hrun?

    Thanks,
    Shrey

  • Shrey_SShrey_S Member

    sorry for the extra bold characters, thats by mistake.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hey Shrey,

    Tandem repeats and homopolymer runs are not defined the same way (within GATK at least). Tandem repeats are repetitions of two or more nucleotides in succession (like ATATATAT), while homopolymers are runs of all the same nucleotide (like AAAAAA). So these annotations are not interchangeable.

  • Shrey_SShrey_S Member
    edited June 2013

    Oh I see. So is HRun annotation feature totally eliminated from the GATK tool?
    Is it possible to bring it back. Its kind of important in our analysis to detect the variants which are annotated with higher HRun values so that they could be filtered out.

  • Shrey_SShrey_S Member

    Alright Geraldine. Thank you so much for your responses..:)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    HRun stands for Homopolymer Run. That's when you have AAAAAAAAA in your sequence, for example.

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