This is a test version of Biostars. For the public version, visit https://www.biostars.org.
g.vcf file with different FORMAT (GT:AD:DP:GQ:PL:SB vs GT:DP:GQ:MIN_DP:PL)

Dear all, I would like to understand why in g.vcf file some rows do have AD values (GT:AD:DP:GQ:PL:SB), some do not (GT:DP:GQ:MIN_DP:PL). I need to get GT,AD,DP values of the individuals, and some variant have . instead of an AD value.

    chr1    865435  .       C       <NON_REF>       .       .       END=865438      GT:DP:GQ:MIN_DP:PL      0/0:66:99:65:0,120,1800
    chr1    865439  .       G       C,<NON_REF>     0       .       DP=12;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=43200.00       GT:AD:DP:GQ:PL:SB  0/0:12,0,0:12:35:0,35,349,35,349,349:9,3,0,0
    chr1    865440  .       G       <NON_REF>       .       .       END=865466      GT:DP:GQ:MIN_DP:PL      0/0:79:99:72:0,100,1800
    chr1    865467  .       A       <NON_REF>       .       .       END=865467      GT:DP:GQ:MIN_DP:PL      0/0:82:13:82:0,13,1378
    chr1    865468  .       C       <NON_REF>       .       .       END=865469      GT:DP:GQ:MIN_DP:PL      0/0:92:99:92:0,120,1800
    chr1    865470  .       T       A,<NON_REF>     0       .       DP=15;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=54000.00       GT:AD:DP:GQ:PL:SB  0/0:13,0,0:13:35:0,35,267,35,267,267:4,9,0,0
    chr1    865471  .       T       <NON_REF>       .       .       END=865473      GT:DP:GQ:MIN_DP:PL      0/0:94:99:92:0,120,1800
    chr1    865474  .       T       <NON_REF>       .       .       END=865474      GT:DP:GQ:MIN_DP:PL      0/0:89:15:89:0,15,2038
    chr1    865483  .       G       <NON_REF>       .       .       END=865487      GT:DP:GQ:MIN_DP:PL      0/0:105:99:103:0,120,1800
    chr1    865488  .       A       C,<NON_REF>     0       .       DP=29;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;RAW_MQ=104400.00      GT:AD:DP:GQ:PL:SB  0/0:29,0,0:29:82:0,82,734,82,734,734:15,14,0,0
    chr1    865489  .       C       <NON_REF>       .       .       END=865490      GT:DP:GQ:MIN_DP:PL      0/0:110:99:109:0,120,1800
    chr1    865491  .       T       A,<NON_REF>     0       .       BaseQRankSum=-1.234;ClippingRankSum=0.000;DP=33;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=0.000;RAW_MQ=118800.00;ReadPosRankSum=1.052 GT:AD:DP:GQ:PL:SB       0/0:32,1,0:33:83:0,83,796,90,799,806:16,16,0,1
vcf
• 1,919 views • link
written by User000 User000

I need to get GT,AD,DP values of the individuals, and some variant have .

why using a g.vcf when you can use a plain vcf ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I do use plain vcf, after doing genotype gvcf, and i still do not get AD values for some variants.

• 0 views • link
written by User000 User000

0 answers

No answers yet.

Log in to answer this question.

More posts like this