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Regarding Different genotypes for same sample using Unified Genotyper & Haplotype Caller

tahseentahseen IGIB,New DelhiMember

Hello Team,

I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples from both the callers.
Which to rely upon for further analysis???

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @tahseen

    Would you please give us some more information.
    Version of GATK you are using? The exact command you are using?
    Would you please post records of the SNP you mentioned. Thank you!

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    We haven't heard from the user in more than two business days. The user has been notified and this ticket is now closed.

  • tahseentahseen IGIB,New DelhiMember

    Hi bhanu

    Sorry for late reply.my question still remains the same.I am posting genotype calls for one of my SNP from both the callers along with the sampleid. Kindly have a look

    caller #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
    haplotype caller 19 54311090 rs11084300 C T 5645.25 . AC=51;AF=0.464;AN=110;BaseQRankSum=1.35;ClippingRankSum=0.00;DB;DP=328;ExcessHet=0.0210;FS=10.016;InbreedingCoeff=0.2385;MLEAC=56;MLEAF=0.509;MQ=52.00;MQRankSum=-1.559e+00;QD=24.54;ReadPosRankSum=0.00;SOR=2.200 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:147,12,0 0/1:4,3:7:85:85,0,111 ./.:0,0:0:.:0,0,0 1/1:0,11:11:33:373,33,0 1/1:0,9:9:27:320,27,0 1/1:0,2:2:6:71,6,0 0/0:1,0:1:3:0,3,11 0/1:3,6:9:63:180,0,63 1/1:0,5:5:15:173,15,0 0/0:6,0:6:0:0,0,29 0/0:4,0:4:12:0,12,103 0/1:2,6:8:41:193,0,41 0/0:7,0:7:21:0,21,222 0/0:2,0:2:6:0,6,48 1/1:0,2:2:6:72,6,0 ./.:0,0:0:.:0,0,0 1/1:0,7:7:21:261,21,0 0/0:5,0:5:15:0,15,140 1/1:0,6:6:18:203,18,0 1/1:0,10:10:30:317,30,0 1/1:0,15:15:45:484,45,0 1/1:0,11:11:33:357,33,0 0/0:4,0:4:9:0,9,135 ./.:0,0:0:.:0,0,0 ./.:0,0:0:.:0,0,0 0/0:9,0:9:27:0,27,281 0/1:3,3:6:62:62,0,85 0/0:6,0:6:18:0,18,214 1/1:0,2:2:6:66,6,0 0/1:3,6:9:66:184,0,66 1/1:0,12:12:36:425,36,0 0/0:8,0:8:24:0,24,262 0/0:3,0:3:9:0,9,77 0/1:2,4:6:46:123,0,46 ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:143,12,0 0/0:2,0:2:0:0,0,1 0/0:3,0:3:0:0,0,27 1/1:0,6:6:18:210,18,0 0/0:3,0:3:9:0,9,90 0/0:3,0:3:9:0,9,98 0/1:6,2:8:45:45,0,176 0/1:4,2:6:50:50,0,122 0/1:1,3:4:20:92,0,20 0/0:4,0:4:12:0,12,120 0/1:1,2:3:21:62,0,21 0/0:4,0:4:0:0,0,60 0/0:1,0:1:3:0,3,24 1/1:0,3:3:9:106,9,0 0/0:5,0:5:0:0,0,101 ./.:0,0:0:.:0,0,0 ./.:2,0:2:.:0,0,0 0/0:4,0:4:0:0,0,66 0/1:3,3:6:73:83,0,73 0/0:6,0:6:18:0,18,188 0/1:2,5:7:47:152,0,47 ./.:1,0:1:.:0,0,0 0/1:3,5:8:70:152,0,70 0/1:5,5:10:99:143,0,116 0/0:3,0:3:0:0,0,31 ./.:0,0:0:.:0,0,0 1/1:0,9:9:27:312,27,0 ./.:0,0:0:.:0,0,0 0/1:6,7:13:99:170,0,163 ./.:0,0:0:.:0,0,0 1/1:0,2:2:6:68,6,0
    unified genotyper 19 54311090 rs11084300 C T 5781.53 . AC=61;AF=0.526;AN=116;BaseQRankSum=11.126;DB;DP=342;Dels=0.00;ExcessHet=0.2545;FS=0.000;HaplotypeScore=0.2680;InbreedingCoeff=0.1031;MLEAC=62;MLEAF=0.534;MQ=53.53;MQ0=0;MQRankSum=-9.532;QD=23.99;ReadPosRankSum=0.877;SOR=0.704 GT:AD:DP:GQ:PL ./.:.:.:.:. 1/1:1,4:5:12:144,12,0 0/1:4,3:7:84:84,0,110 ./.:.:.:.:. 1/1:0,11:11:33:369,33,0 1/1:0,9:9:27:315,27,0 1/1:0,2:2:6:70,6,0 0/0:1,0:1:3:0,3,33 0/1:3,6:9:63:178,0,63 1/1:0,5:5:15:171,15,0 0/1:3,3:6:49:49,0,90 0/0:4,0:4:12:0,12,130 0/1:2,7:9:38:221,0,38 0/0:8,0:8:24:0,24,265 0/0:4,0:4:12:0,12,130 1/1:0,2:2:6:70,6,0 ./.:.:.:.:. 1/1:0,7:7:21:256,21,0 0/0:7,0:7:21:0,21,221 1/1:0,6:6:18:200,18,0 1/1:0,10:10:27:304,27,0 1/1:0,15:15:42:469,42,0 1/1:0,11:11:30:343,30,0 0/0:4,0:4:12:0,12,125 ./.:.:.:.:. ./.:.:.:.:. 0/0:9,0:9:27:0,27,283 0/1:4,3:7:52:52,0,115 0/0:9,0:9:27:0,27,277 1/1:0,2:2:6:66,6,0 0/1:3,6:9:66:181,0,66 1/1:0,14:14:36:419,36,0 0/0:8,0:8:24:0,24,260 0/0:4,0:4:12:0,12,112 0/1:2,4:6:46:121,0,46 ./.:.:.:.:. 1/1:0,4:4:12:141,12,0 0/1:1,1:2:25:25,0,26 0/1:2,1:3:24:24,0,54 1/1:0,6:7:18:207,18,0 0/0:3,0:3:9:0,9,97 0/0:3,0:3:9:0,9,97 0/1:6,2:8:45:45,0,173 0/1:4,2:6:50:50,0,120 0/1:1,3:4:20:91,0,20 0/0:4,0:4:12:0,12,121 0/1:1,2:3:21:61,0,21 0/1:3,1:4:21:21,0,84 0/0:1,0:1:3:0,3,27 1/1:0,3:3:9:105,9,0 0/1:4,1:5:18:18,0,118 ./.:.:.:.:. 0/1:1,1:2:27:29,0,27 0/1:3,1:4:21:21,0,86 0/1:3,3:6:73:82,0,73 0/0:6,0:6:18:0,18,190 0/1:2,5:7:47:150,0,47 1/1:0,1:1:3:33,3,0 0/1:3,5:8:70:149,0,70 0/1:5,5:10:99:144,0,113 0/1:2,1:3:24:24,0,57 0/0:1,0:1:3:0,3,32 1/1:0,9:9:27:308,27,0 ./.:.:.:.:. 0/1:6,7:13:99:167,0,164 ./.:.:.:.:. 1/1:0,2:2:6:68,6,0

    If you notice, my sampleid's 11,38,39,48,51,53,54,58,61,62 are having discordant genotypes in both callers

    **Commands used for Haplotype caller **

    For generating g,vcf
    java -jar GenomeAnalysisTK.jar \
    -R reference.fasta \
    -T HaplotypeCaller \
    -I sample1.bam \
    --emitRefConfidence GVCF \
    [--dbsnp dbSNP.vcf] \
    [-L targets.interval_list] \
    -o output.raw.snps.indels.g.vcf

    & then combining g.vcf using GenotypeGVCFs tool (all default parameters)

    Command used for unified genotyper

    java -jar GenomeAnalysisTK.jar \
    -R reference.fasta \
    -T UnifiedGenotyper \
    -I sample1....67.bam \
    -stand_call_conf 40.0 \
    --dbsnp dbSNP.vcf\
    -L targets.interval_list]\
    -o output.vcf

  • tahseentahseen IGIB,New DelhiMember

    Hi bhanu

    I have mentioned the details in above post.Sorry for the delayed reply.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited April 29

    Hi @tahseen

    Looks like you are using HaplotypeCaller from GATK3. We do no support GATK3 anymore. And UnifiedGenotyper is not in GATK4 either.

    Please use the latest version GATK4.1.2.0

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