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CombineGVCFs with gvcf processed by samtools/bcftools

lindenblindenb FranceMember ✭✭
edited April 2015 in Ask the GATK team

Hi GATK team,
I've tried to use the gvcf produced by samtools/bcftools.
Here is a snapshot of my Makefile for the calling part:

define gvcf_samtools_haloplex


$(1): $(2) $(3)
        mkdir -p $$(dir [email protected])   &&       $${samtools.exe}  mpileup  --uncompressed --BCF --output-tags DP,DV,DP4,SP  --redo-BAQ --adjust-MQ 50 --min-ireads 3 --gap-frac 0.00
2  --min-MQ 30 --fasta-ref $$(REF)              --max-depth 10000               --max-idepth 10000              $$(if $$(filter %.bed,$$^),--positions $$(filter %.bed,$$^),
)               --count-orphans                 $$<  |  $${bcftools.exe} call  --gvcf 20  --output-type v --variants-only --multiallelic-caller --format-fields GQ,GP   -o $
$(addsuffix .tmp.vcf,[email protected]) -  &&         mv $$(addsuffix .tmp.vcf,[email protected])  [email protected]


endef

when the gvcf files are used by CombineGVCFs, I get the following exception:

java -jarGenomeAnalysisTK.jar -T CombineGVCFs             -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta --variant OUTDIR/Projects/bigone/VCF/__DELETE__bigone2015.bigone.samtools.gvcf.list              -S SILENT -o OUTDIR/Projects/bigone/VCF/__DELETE__bigone2015.bigone.samtools.combined.g.vcf.tmp.vcf
dynamic mode

INFO  09:39:55,978 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:39:55,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO  09:39:55,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:39:55,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:39:55,989 HelpFormatter - Program Args: -T CombineGVCFs -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta --variant OUTDIR/Projects/bigone/VCF/__DELETE__bigone2015.bigone.samtools.gvcf.list -S SILENT -o OUTDIR/Projects/bigone/VCF/__DELETE__bigone2015.bigone.samtools.combined.g.vcf.tmp.vcf
INFO  09:39:55,994 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19.
INFO  09:39:55,995 HelpFormatter - Date/Time: 2015/04/14 09:39:55
INFO  09:39:55,995 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:39:55,996 HelpFormatter - --------------------------------------------------------------------------------
INFO  09:39:58,104 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:39:58,269 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  09:40:18,824 GenomeAnalysisEngine - Preparing for traversal
INFO  09:40:18,859 GenomeAnalysisEngine - Done preparing for traversal
INFO  09:40:18,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  09:40:18,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  09:40:18,862 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 32768065 is less than start 32768066 in contig 1
##### ERROR ------------------------------------------------------------------------------------------

here is a snapshot of the gvcf contaning 32768065:

 cat __DELETE__bigone2015.bigone.samtools.gvcf.list | xargs cut -f2,4,5,8 | grep -whF -A1 -B1 32768066


32757721        G       .       END=32757891
32768025        A       .       END=32768065
32768066        T       .       END=32768065
32768066        TC      T       INDEL;IDV=36;IMF=0.349515;DP=100;VDB=5.37817e-15;SGB=-0.693054;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,0,28,0;MQ=49
32768067        C       T       DP=61;VDB=1.14947e-07;SGB=-0.688148;RPB=0.0443614;MQB=0.986249;BQB=0.0581566;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=10,0,15,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=107;VDB=1.27981e-36;SGB=-0.693147;RPB=0.145801;MQB=0.659702;BQB=0.0567542;MQ0F=0;AC=2;AN=2;DP4=11,0,51,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=82;VDB=6.85164e-21;SGB=-0.693146;RPB=0.825581;MQB=0.697674;BQB=0.883721;MQ0F=0;AC=2;AN=2;DP4=2,0,43,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=84;VDB=7.44212e-14;SGB=-0.693145;RPB=0.030182;MQB=0.575018;BQB=0.0531329;MQ0F=0;AC=2;AN=2;DP4=6,0,41,0;MQ=48
--
32768025        A       .       END=32768064
32768065        T       C       DP=122;VDB=4.86965e-13;SGB=-0.692067;RPB=0.409269;MQB=0.707596;BQB=0.00055632;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=30,0,20,0;MQ=48
32768065        T       .       END=32768066
32768067        C       T       DP=106;VDB=1.4115e-10;SGB=-0.693054;RPB=0.0329847;MQB=0.883119;BQB=0.647624;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=19,0,28,0;MQ=49
--
32757679        C       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=157;VDB=2.99447e-25;SGB=-0.693147;RPB=0.446601;MQB=0.783611;BQB=0.323437;MQ0F=0;AC=2;AN=2;DP4=9,0,77,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=91;VDB=1.91056e-12;SGB=-0.693147;RPB=0.921275;MQB=0.857999;BQB=0.380388;MQ0F=0;AC=2;AN=2;DP4=6,0,49,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=35;VDB=1.38853e-08;SGB=-0.69168;RPB=0.524801;MQB=0.979651;BQB=0.524801;MQ0F=0;AC=2;AN=2;DP4=4,0,19,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=76;VDB=2.26381e-08;SGB=-0.693136;RPB=0.0423819;MQB=0.639856;BQB=0.0341585;MQ0F=0;AC=2;AN=2;DP4=7,0,35,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=63;VDB=2.20811e-09;SGB=-0.692976;RPB=0.170874;MQB=0.722875;BQB=0.0252673;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,0,26,0;MQ=49
--
32757684        C       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=40;VDB=6.04185e-10;SGB=-0.689466;RPB=0.25;MQB=0.9375;BQB=0.25;MQ0F=0;AC=2;AN=2;DP4=2,0,16,0;MQ=49
--
32757679        C       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=207;VDB=2.1795e-29;SGB=-0.693147;RPB=0.00231647;MQB=0.538424;BQB=0.00483428;MQ0F=0;AC=2;AN=2;DP4=13,0,99,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=43;VDB=1.23981e-07;SGB=-0.683931;MQ0F=0;AC=2;AN=2;DP4=0,0,13,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=28;VDB=3.51673e-06;SGB=-0.688148;RPB=0.333333;MQB=0.8;BQB=0.466667;MQ0F=0;AC=2;AN=2;DP4=2,0,15,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=38;VDB=3.77934e-07;SGB=-0.691153;RPB=0.173145;MQB=0.877714;BQB=0.32969;MQ0F=0;AC=2;AN=2;DP4=4,0,18,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=38;VDB=4.5048e-09;SGB=-0.692562;RPB=0.729381;MQB=0.881726;BQB=0.0429872;MQ0F=0;AC=2;AN=2;DP4=3,0,22,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768065
32768066        TC      T       INDEL;IDV=30;IMF=0.309278;DP=92;VDB=4.68847e-13;SGB=-0.693097;MQ0F=0;AC=2;AN=2;DP4=6,0,30,0;MQ=48
32768067        C       T       DP=61;VDB=0.00740154;SGB=-0.616816;RPB=0.231146;MQB=0.924584;BQB=0.924584;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,6,0;MQ=49
--
32757892        C       T       DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=50
32768025        A       .       END=32768066
32768067        C       T       DP=43;VDB=2.52435e-11;SGB=-0.692831;RPB=0.913904;MQB=0.953497;BQB=0.604728;MQ0F=0;AC=2;AN=2;DP4=3,0,24,0;MQ=48
--
32768025        A       .       END=32768050
32768066        TC      T       INDEL;IDV=4;IMF=0.153846;DP=26;VDB=1.68071e-06;SGB=-0.556411;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=7,0,4,0;MQ=48
32768067        C       T       DP=22;VDB=0.154358;SGB=-0.511536;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=48
--
32757688        T       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=106;VDB=5.33136e-17;SGB=-0.693147;MQ0F=0;AC=2;AN=2;DP4=0,0,50,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=52;VDB=2.64783e-06;SGB=-0.691153;RPB=0.78077;MQB=0.922371;BQB=0.0374746;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,18,0;MQ=48
--
32768025        A       .       END=32768050
32768051        T       .       END=32768066
32768067        C       T       DP=27;VDB=1.18758e-07;SGB=-0.690438;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,17,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768065
32768067        C       T       DP=35;VDB=0.00415585;SGB=-0.683931;RPB=0.0851108;MQB=0.832553;BQB=0.0731397;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,13,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=96;VDB=4.21707e-19;SGB=-0.693147;RPB=0.429291;MQB=0.986088;BQB=0.00988274;MQ0F=0;AC=2;AN=2;DP4=7,0,47,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768068        T       .       END=32768071
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=35;VDB=5.3147e-08;SGB=-0.69168;RPB=0.605263;MQB=0.736842;BQB=0.157895;MQ0F=0;AC=2;AN=2;DP4=2,0,19,0;MQ=49
--
32757645        A       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=111;VDB=1.28269e-05;SGB=-0.69168;RPB=0.0468862;MQB=0.524801;BQB=0.573544;MQ0F=0;AC=2;AN=2;DP4=4,0,19,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=29;VDB=0.000228416;SGB=-0.676189;RPB=0.646383;MQB=0.782349;BQB=0.092944;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,11,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=61;VDB=2.08113e-07;SGB=-0.693054;RPB=0.333887;MQB=0.808136;BQB=0.724199;MQ0F=0;AC=2;AN=2;DP4=5,0,28,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=26;VDB=1.62429e-07;SGB=-0.676189;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,11,0;MQ=50
--
32768025        A       .       END=32768050
32768066        TC      T       INDEL;IDV=4;IMF=0.173913;DP=22;VDB=0.0270423;SGB=-0.556411;MQ0F=0;AC=2;AN=2;DP4=1,0,4,0;MQ=48
32768068        T       .       END=32768070
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=57;VDB=9.28657e-08;SGB=-0.691153;RPB=0.0307499;MQB=0.969233;BQB=0.0900137;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=8,0,18,0;MQ=49
--
32757721        G       .       END=32757891
32768025        A       .       END=32768065
32768066        TC      T       INDEL;IDV=10;IMF=0.204082;DP=49;VDB=1.28199e-08;SGB=-0.651104;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=14,0,8,0;MQ=47
32768067        C       T       DP=39;VDB=0.0505719;SGB=-0.636426;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,7,0;MQ=47
--
32757645        A       .       END=32757891
32768025        A       .       END=32768065
32768066        TC      T       INDEL;IDV=23;IMF=0.164286;DP=136;VDB=5.53751e-13;SGB=-0.692067;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=13,0,20,0;MQ=48
32768067        C       T       DP=113;VDB=0.00011222;SGB=-0.686358;RPB=0.0294684;MQB=0.816272;BQB=0.38558;MQ0F=0;AC=2;AN=2;DP4=4,0,14,0;MQ=49
--
32768025        A       .       END=32768062
32768064        T       .       END=32768066
32768067        C       T       DP=31;VDB=2.8024e-07;SGB=-0.680642;RPB=0.861658;MQB=0.767432;BQB=0.913864;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,0,12,0;MQ=49
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=186;VDB=2.94273e-44;SGB=-0.693147;RPB=0.000575688;MQB=0.642812;BQB=0.0982708;MQ0F=0;AC=2;AN=2;DP4=14,0,106,0;MQ=47
--
32757722        G       .       END=32757891
32768026        A       .       END=32768065
32768066        T       .       END=32768065
32768066        TC      T       INDEL;IDV=42;IMF=0.488372;DP=83;VDB=5.40575e-21;SGB=-0.693145;MQ0F=0;AC=2;AN=2;DP4=7,0,40,0;MQ=49
32768067        C       T       DP=41;VDB=0.000382795;SGB=-0.651104;RPB=0.0172892;MQB=0.562066;BQB=0.959099;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,8,0;MQ=48
--
32768026        A       .       END=32768064
32768065        T       C       DP=46;VDB=4.85251e-07;SGB=-0.686358;RPB=0.670716;MQB=0.958545;BQB=0.000568099;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=16,0,14,0;MQ=49
32768066        T       .       END=32768066
32768068        T       .       END=32768073
--
32757722        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=34;VDB=1.38418e-05;SGB=-0.688148;RPB=0.7;MQB=0.933333;BQB=0.933333;MQ0F=0;AC=2;AN=2;DP4=2,0,15,0;MQ=48
--
32757722        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=75;VDB=2.16734e-11;SGB=-0.693136;RPB=0.00921987;MQB=0.811936;BQB=0.82152;MQ0F=0;AC=2;AN=2;DP4=6,0,35,0;MQ=48
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=46;VDB=1.10418e-07;SGB=-0.693079;RPB=0.181374;MQB=0.964868;BQB=0.981262;MQ0F=0;AC=2;AN=2;DP4=5,0,29,0;MQ=47
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=43;VDB=1.27519e-12;SGB=-0.692976;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,26,0;MQ=49
--
32757680        C       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=46;VDB=2.72057e-11;SGB=-0.692717;RPB=0.903753;MQB=0.354771;BQB=0.971625;MQ0F=0;AC=2;AN=2;DP4=5,0,23,0;MQ=49
--
32768026        A       .       END=32768060
32768066        T       .       END=32768066
32768067        C       T       DP=30;VDB=2.04238e-07;SGB=-0.690438;RPB=0.987474;MQB=0.892753;BQB=0.283511;MQ0F=0;AC=2;AN=2;DP4=3,0,17,0;MQ=48
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=62;VDB=2.44263e-09;SGB=-0.693054;MQ0F=0;AC=2;AN=2;DP4=0,0,28,0;MQ=48
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=134;VDB=7.06062e-26;SGB=-0.693147;RPB=0.000880621;MQB=0.588454;BQB=0.670928;MQ0F=0;AC=2;AN=2;DP4=10,0,75,0;MQ=48
--
32757680        C       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=52;VDB=9.35919e-11;SGB=-0.692831;RPB=0.114218;MQB=0.845852;BQB=0.651439;MQ0F=0;AC=2;AN=2;DP4=3,0,24,0;MQ=48
--
32768025        A       .       END=32768050
32768051        T       .       END=32768066
32768067        C       T       DP=29;VDB=8.52499e-06;SGB=-0.691153;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,18,0;MQ=48
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=220;VDB=0;SGB=-0.693147;RPB=0.167013;MQB=0.427009;BQB=0.162397;MQ0F=0;AC=2;AN=2;DP4=19,0,125,0;MQ=48
--
32757646        G       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=50;VDB=1.56275e-05;SGB=-0.690438;RPB=0.170712;MQB=0.860378;BQB=0.801124;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,0,17,0;MQ=48
--
32768025        A       .       END=32768050
32768051        T       .       END=32768066
32768067        C       T       DP=35;VDB=1.06013e-06;SGB=-0.686358;MQ0F=0;AC=2;AN=2;DP4=0,0,14,0;MQ=49
--
32757888        G       .       END=32757891
32768065        T       C       DP=18;VDB=0.0221621;SGB=-0.511536;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,3,0;MQ=50
32768066        TC      T       INDEL;IDV=5;IMF=0.277778;DP=18;VDB=0.00021572;SGB=-0.616816;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,0,6,0;MQ=49
32768188        T       .       END=32768247
--
32757680        C       .       END=32757891
32768026        A       .       END=32768066
32768067        C       T       DP=93;VDB=1.22543e-26;SGB=-0.693147;RPB=0.405658;MQB=0.999512;BQB=0.69141;MQ0F=0;AC=2;AN=2;DP4=4,0,53,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=51;VDB=1.59314e-10;SGB=-0.692067;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,20,0;MQ=48
--
32757888        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=51;VDB=0.00037052;SGB=-0.683931;RPB=0.48045;MQB=0.832553;BQB=0.641825;MQ0F=0;AC=2;AN=2;DP4=3,0,13,0;MQ=48
--
32757679        C       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=72;VDB=0.000573512;SGB=-0.686358;RPB=1;MQB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=1,0,14,0;MQ=48
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=48;VDB=0.0303686;SGB=-0.616816;RPB=0;MQB=0.666667;BQB=0.333333;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,0,6,0;MQ=48
--
32757645        A       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=63;VDB=9.36785e-08;SGB=-0.692352;RPB=0.0501991;MQB=0.673273;BQB=0.606114;MQ0F=0;AC=2;AN=2;DP4=4,0,21,0;MQ=48
--
32768025        A       .       END=32768050
32768051        T       .       END=32768065
32768066        T       .       END=32768065
32768066        TC      T       INDEL;IDV=9;IMF=0.166667;DP=51;VDB=0.000464403;SGB=-0.636426;MQ0F=0;AC=2;AN=2;DP4=1,0,7,0;MQ=48
32768067        C       T       DP=40;VDB=3.93392e-06;SGB=-0.689466;RPB=0.602752;MQB=0.602752;BQB=0.855345;MQ0F=0;AC=2;AN=2;DP4=3,0,16,0;MQ=47
--
32757721        G       .       END=32757891
32768025        A       .       END=32768066
32768067        C       T       DP=56;VDB=3.41847e-09;SGB=-0.693097;RPB=0.995312;MQB=0.968732;BQB=0.183337;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=7,0,30,0;MQ=48

is it a problem with GATK or samtools ?

thanks !

Pierre

Best Answer

Answers

  • lindenblindenb FranceMember ✭✭

    thank you Geraldine

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