Question: Mpileup Multiple Samples - Individual DP Values
0
gravatar for Ks-seq
4 months ago by
Ks-seq10
Ks-seq10 wrote:

Hi I used mpileup (samtools and bcftools) for multiple samples (.bam files), and found that there is only single INFO field providing values for DP,AD etc. If I use single .bam file then INFO field is for single sample, that is quite clear:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  chr1.bam
1   629150  .   G   T   3.22451 .   DP=19;ADF=0,10;ADR=0,9;AD=0,19;VDB=0.000446291;SGB=-0.69168;MQSB=0.992528;MQ0F=0.315789;AC=2;AN=2;DP4=0,0,10,9;MQ=0 GT:PL:DP:SP:ADF:ADR:AD:GP:GQ    1/1:30,57,0:19:0:0,10:0,9:0,19:-2.14748e+09,-2.14748e+09,0:127

However, using multiple samples I get like this:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  chr1.bam    chr12.bam
1   629136  .   G   C   4.79824 .   DP=19;ADF=0,10;ADR=0,9;AD=0,19;VDB=0.000613736;SGB=10.4471;MQSB=0.992528;MQ0F=0.315789;AC=2;AN=2;DP4=0,0,10,9;MQ=0  GT:PL:DP:SP:ADF:ADR:AD:GP:GQ    1/1:30,57,0:19:0:0,10:0,9:0,19:-2.14748e+09,-2.14748e+09,0:127  ./.:0,0,0:0:0:0,0:0,0:0,0:0,0,0:0

What is the relation of DP, AD values here with my samples (chr1.bam and ch12.bam) ? I was wondering whether it is possible to get DP,AD values for each individual? Similar question was asked years ago but no proper answer :( Mpileup Multiple Samples - Individual Dp4 Values
Thank you.

rna-seq snp alignment • 177 views
ADD COMMENTlink modified 4 months ago by Pierre Lindenbaum129k • written 4 months ago by Ks-seq10
0
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

DP, AD values here

so we have two genotypes with a DP field (the 3rd). and the AD field (7th)

  GT:PL:DP:SP:ADF:ADR:AD:GP:GQ    1/1:30,57,0:19:0:0,10:0,9:0,19:-2.14748e+09,-2.14748e+09,0:127  ./.:0,0,0:0:0:0,0:0,0:0,0:0,0,0:0

there is no call for the 2nd genotype

1st genotype is DP=19 and AD=0,19 (0 read matching REF, 19 reads matching ALT)

in the INFO field, the sum of genotypes DPs is 19, the sum of genotypes ADs is 0,19

ADD COMMENTlink written 4 months ago by Pierre Lindenbaum129k

Thanks for reply. Does it mean that INFO filed is sum of 1st and 2nd genotype i.e. DP=19 of chr1.bam + DP=0 of chr1.bam = total DP=19 in INFO field ?

ADD REPLYlink written 4 months ago by Ks-seq10

yes .

ADD REPLYlink written 4 months ago by Pierre Lindenbaum129k

Thanks, Is there anyway to seperate INFO field for each ? It will not be standard vcf file, however, if it is possible?

ADD REPLYlink written 4 months ago by Ks-seq10
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