Question: Samtools mpileup genotype likelihood no PL field when all individuals are 0/0
0
gravatar for cetin.m
20 months ago by
cetin.m50
cetin.m50 wrote:

I am calling SNPS using samtools with the command:

samtools mpileup -g -uf /mnt/NAS/share/Ref/human/hg19_chr/Chr_all.fa -l 1000G_D10KApart2.bed -q 15 -Q 20 -b CEPHbam.list -o CEPH_1000G_10Kapart.bcf

I have 5 individuals in CEPHbam.list I am giving a reference SNP list in the file 1000G_D10KApart2.bed

My problem is as follows:

For the positions that are 0/0 for all 5 individuals, I get no PL field.

For ex: chr1 66715 . A . 966 . DP=98;MQSB=0.00315921;MQ0F=0;AN=10;DP4=78,18,0,0;MQ=28 GT 0/0 0/0 0/0 0/0 0/0

OR chr1 46650 . T . 558 . DP=109;MQSB=0.998858;MQ0F=0;AN=6;DP4=60,46,0,0;MQ=19 GT 0/0 0/0 ./. 0/0 ./.

What I need is this: chr1 691544 . T A 999 . DP=147;VDB=0.00863476;SGB=-18.2072;RPB=0.999674;MQB=0.941943;MQSB=0.997675;BQB=0.999976;MQ0F=0;ICB=0.724138;HOB=0.18;AC=7;AN=10;DP4=19,27,47,42;MQ=35 GT:PL 0/1:236,0,255 1/1:255,49,0 0/1:90,0,199 1/1:255,69,0 0/1:244,0,218

In short, I need the PL field to be shown for all positions.

How can I achieve this?

mpileup samtools pl • 742 views
ADD COMMENTlink modified 20 months ago by Santosh Anand5.1k • written 20 months ago by cetin.m50
0
gravatar for Santosh Anand
20 months ago by
Santosh Anand5.1k
Santosh Anand5.1k wrote:

0/0 in all samples implies there are only REF alleles and no ALT allele is present. The PL is calculated as the probability of ALT alleles and given as a PHRED-like score (https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it). Since there are no ALT alleles in your data (note that there is a dot in ALT column too), the PL is missing. Usually, you should not keep these lines in the VCF file as they will unnecessary bloat the size of your VCF.

ADD COMMENTlink written 20 months ago by Santosh Anand5.1k
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