I'm trying to achieve what this post was looking for https://www.biostars.org/p/77012/ 

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!

Hi, you can specify this via the `mpileup` command. Please take a look at this snippet from my historical pipeline:

 - <a href="https://github.com/kevinblighe/ClinicalGradeDNAseq/blob/master/AnalysisMasterVersion1.sh#L300-L316">ClinicalGradeDNAseq#L300-L316</a>

That is:

    bcftools mpileup \
      --redo-BAQ \
      --min-BQ 30 \
      --per-sample-mF \
      --annotate FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR \
      -f "${Ref_FASTA}" \
      Aligned_Sorted_PCRDuped_FiltMAPQ.bam |\
      bcftools call \
        --multiallelic-caller \
        --variants-only \
        -Ob > Aligned_Sorted_PCRDuped_FiltMAPQ.bcf ;

Kevin