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