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error CombineVariants UNIQUIFY

pachchekpachchek franceMember
edited January 2017 in Ask the GATK team

Hello,

I am trying to merge 2 vcf for same sample with 2 different caller (like GATK UG and HC)
I use CombineVariants tools with -genotypeMergeOptions UNIQUIFY option.
comande line :
java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg19.fa --variant:SampleX_gatkHC SampleID_gatkHC.vcf --variant:SampleX_gatkUG SampleX_gatkUG.vcf -o SampleX.full.vcf -genotypeMergeOptions UNIQUIFY

SampleX_gatkHC.vcf :
GT:AD:DP:GQ:PL 1/2:7,53,18:78:99:2512,426,875,1811,0,2040

SampleX_gatkUG.vcf :
GT:AD:DP:GQ:PL 1/2:11,29,71:175:99:6052,4932,6910,983,0,367

SampleX.full.vcf :
FORMAT SampleX_gatkHC.vcf SampleX_gatkUG.vcf
GT:DP:GQ 1/2:78:99 2/1:175:99

why we loste some information like AD GQ PL ?

the format that I want is :
FORMAT SampleX_gatkHC.vcf SampleX_gatkUG.vcf
GT:AD:DP:GQ:PL 1/2:7,53,18:78:99:2512,426,875,1811,0,2040 1/2:11,29,71:175:99:6052,4932,6910,983,0,367

Can you help me to solve the problem.
I use GATK ( version : 3.5-0) and java (1.8.0_65)

Thanks

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @pachchek
    Hi,

    I just tried the same command on some test files, and I get proper results (without any loss of information). Perhaps try adding --never_trim_vcf_format_field to your command. Does this occur at all sites, or just a few?

    Thanks,
    Sheila

  • pachchekpachchek franceMember
    edited January 2017

    Hello Sheila,
    Thanks for your help.
    I try with the option --never_trim_vcf_format_field and I have the same result.
    This problem occur just for few particular variant.
    I do a test with synthetic vcf.

    SampleX_gatkUG.vcf : the output vcf with GATK UG caller

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PATIENT_X

    chr2 73613031 . TGGAGGA TGGAGGAGGA,T 6014.73 PASS . GT:AD:DP:GQ:PL 1/2:11,29,71:175:99:6052,4932,6910,983,0,3676
    chr2 73613035 . TGGAGGA TGGAGGAGGA,T 6014.73 PASS . GT:AD:DP:GQ:PL 1/2:11,164,0:175:99:6052,4932,6910,983,0,3676
    chr2 73613040 . TGGAGGA TGGAGGAGGA,T 6014.73 PASS . GT:AD:DP:GQ:PL 1/2:11,0,164:175:99:6052,4932,6910,983,0,3676
    chr2 73613045 . TGGAGGA TGGAGGAGGA,T 6014.73 PASS . GT:AD:DP:GQ:PL 1/2:0,164,11:175:99:6052,4932,6910,983,0,3676
    chr3 121500485 . TACACACACACACAC T,TACACACACACAC 8146.73 PASS . GT:AD:DP:GQ:PL 1/2:45,10,21:80:99:8184,1158,3814,6354,0,6127
    chr3 121500479 . TACACACACACACAC T,TACACACACACAC 8146.73 PASS . GT:AD:DP:GQ:PL 1/2:0,45,31:80:99:8184,1158,3814,6354,0,6127
    chr3 121500480 . TACACACACACACAC T,TACACACACACAC 8146.73 PASS . GT:AD:DP:GQ:PL 1/2:45,0,31:80:99:8184,1158,3814,6354,0,6127
    chr3 121500490 . TACACACACACACAC T,TACACACACACAC 8146.73 PASS . GT:AD:DP:GQ:PL 1/2:21,55,0:80:99:8184,1158,3814,6354,0,6127

    SampleX_gatkHC.vcf : the output vcf with GATK HC caller

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PATIENT_X

    chr2 73613031 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS . GT:AD:DP:GQ:PL 1/2:7,53,18:78:99:2512,426,875,1811,0,2040
    chr2 73613035 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS . GT:AD:DP:GQ:PL 1/2:7,71,0:78:99:2512,426,875,1811,0,2040
    chr2 73613040 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS . GT:AD:DP:GQ:PL 1/2:7,0,71:78:99:2512,426,875,1811,0,2040
    chr2 73613045 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS . GT:AD:DP:GQ:PL 1/2:0,71,7:78:99:2512,426,875,1811,0,2040
    chr3 121500485 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS . GT:AD:DP:GQ:PL 1/2:52,11,11:74:99:2791,683,976,2169,0,2103
    chr3 121500479 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS . GT:AD:DP:GQ:PL 1/2:0,52,22:74:99:2791,683,976,2169,0,2103
    chr3 121500480 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS . GT:AD:DP:GQ:PL 1/2:52,0,22:74:99:2791,683,976,2169,0,2103
    chr3 121500490 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS . GT:AD:DP:GQ:PL 1/2:11,63,0:74:99:2791,683,976,2169,0,2103

    SampleX.full.vcf : the output vcf after CombineVariants tools
    comande line :
    java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg19.fa --variant:SampleX_gatkHC SampleID_gatkHC.vcf --variant:SampleX_gatkUG SampleX_gatkUG.vcf -o SampleX.full.vcf -genotypeMergeOptions UNIQUIFY --never_trim_vcf_format_field

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ADN150693.bwamem.gatkHC_DIAG_IP.howard ADN150693.bwamem.gatkUG_DIAG_IP.howard

    chr2 73613031 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:DP:GQ 1/2:78:99 2/1:175:99
    chr2 73613035 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:DP:GQ 1/2:78:99 2/1:175:99
    chr2 73613040 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:DP:GQ 1/2:78:99 2/1:175:99
    chr2 73613045 . TGGAGGA T,TGGAGGAGGA 2474.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:DP:GQ 1/2:78:99 2/1:175:99
    chr3 121500485 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:AD:DP:GQ:PL 1/2:52,11,11:74:99:2791,683,976,2169,0,2103 1/2:45,10,21:80:99:8184,1158,3814,6354,0,6127
    chr3 121500479 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:AD:DP:GQ:PL 1/2:0,52,22:74:99:2791,683,976,2169,0,2103 1/2:0,45,31:80:99:8184,1158,3814,6354,0,6127
    chr3 121500480 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:AD:DP:GQ:PL 1/2:52,0,22:74:99:2791,683,976,2169,0,2103 1/2:45,0,31:80:99:8184,1158,3814,6354,0,6127
    chr3 121500490 . TACACACACACACAC T,TACACACACACAC 2753.73 PASS AC=2,2;AF=0.500,0.500;AN=4;set=Intersection GT:AD:DP:GQ:PL 1/2:11,63,0:74:99:2791,683,976,2169,0,2103 1/2:21,55,0:80:99:8184,1158,3814,6354,0,6127

    my test consist to check with different DP for REF and ALT we obtain the correct output for CombineVariants tools.
    The output is correct for chr3 variants but not for chr2.
    can you try with the same vcf ? thanks
    Do you have any solution ?

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