Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )

Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )

1

I’m trying to achieve what this post was looking for Add Dp Tag To Genotype Field Of Vcf File

Currently this is my command:

bcftools mpileup -Ou --max-depth 8000 --min-MQ 30 --min-BQ 30 -f reference.fasta sample1.sorted.bam | bcftools call --ploidy 1 -Ou -mv |  bcftools filter -s LowQual -e '%QUAL<20'  > sample1.flt.vcf

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample1.sorted.bam
Imtechella_halotolerans_length_3113269  4051    .   C   T   41.4148 PASS    DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,0,2;MQ=42  GT:PL   1:71,0
Imtechella_halotolerans_length_3113269  4081    .   C   T   45.4146 PASS    DP=2;VDB=0.02;SGB=-0.453602;MQ0F=0;AC=1;AN=1;DP4=0,0,0,2;MQ=42  GT:PL   1:75,0

As far as I can understand the DP specified in the INFO is depth of coverage across all samples. How can I get the depth per sample info in the format/genotype field?

Any help appreciated!


bcftools


snp


vcf


calling

• 370 views

Read more here: Source link