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VariantsToTable exxtract DP on mutect2 results

I want to obtain from vcf a table with position and DP. I try to use VariantsToTable but There is no wa tooobtin DP values.

##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Nam
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  20
chr1    13417   .       C       CGAGA   .       alt_allele_in_normal    ECNT=2;HCNT=2;MAX_ED=1;MIN_ED=1;NLOD=132.64;RPA=2,4;RU
chr1    13418   .       G       A       .       alt_allele_in_normal    ECNT=2;HCNT=1;MAX_ED=1;MIN_ED=1;NLOD=65.51;TLOD=290.63
chr1    13557   .       G       A       .       alt_allele_in_normal    ECNT=1;HCNT=16;MAX_ED=.;MIN_ED=.;NLOD=151.25;TLOD=42.9
chr1    13557   .       G       A       .       alt_allele_in_normal    ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=204.16;TLOD=84.73
java  -Djava.io.tmpdir=/tmp/  -Xmx3200M -jar   GenomeAnalysisTK.jar  -R  hg19_primary.fa  -T VariantsToTable -V Results/mutect2/432.mutect2.vcf  -F  CHROM -F POS -GF GT  -F TLOD -GF "DP"  -F NLOD   -o results.table 

Unfortunnately I obtain NA value for DP value

CHROM   POS TLOD    NLOD    20.GT   20.DP
chr1    45805566    47.68   10.53   G/G NA
chr1    235543476   7.85    16.18   TTGTGTGTGTGTGT
GTGTGTGTGTG/TTGTGTGTGTGTGTGTGTGTGTGTG   NA
chr1    248637417   14.84   57.24   C/C NA
chr2    46707808    53.42   19.42   C/C NA
chr2    46707808    37.56   79.88   C/C NA
chr3    195509769   6.32    60.69   A/A NA
chr4    367275  6.79    17.75   A/A NA

How can resolve this problems?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mauriziopolano
    Hi,

    There are no DP values in your example VCF. The Mutect2 VCF should have DP values. How did you produce your input VCF? Please post your exact command line and version.

    Thanks,
    Sheila

  • mauriziopolanomauriziopolano udineMember

    thanks for your help. I Use mutect2 (3.6-0-g89b7209)

    java -Xms2g -jar /illumina/software/PROG2/GenomeAnalysisTK.jar -T MuTect2 -R {params.genome} -I:tumor {input[0]} -I:normal {input[1]} --dbsnp {params.dbsnp} --cosmic {params.cosmic} -L {input.target2} -o {output}"

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mauriziopolano
    Hi,

    Hmm. I vaguely remember MuTect2 in GATK3 not outputting the DP. The DP is output in GATK4 Mutect2. Can you try using GATK4 Mutect2?

    Thanks,
    Sheila

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