Missing value in AD (allele depth) in VCF (eg: DP=8, AD=7,.)
Hi, I am using bcftools 1.12 to generate VCFs with the following command (I am working with veeery low coverage data and even low DP sites are of interest at this moment):
bcftools mpileup -q 20 -Q 20 --ignore-RG \
-a FMT/DP,FMT/AD,FORMAT/SCR,FORMAT/SP,INFO/SCR \
-E -f ${REF} -R ${BED} -Ou ${input_BAM} | \
bcftools call --annotate GQ,GP --ploidy 2 -m -Oz -o ${output_VCF}
One variant of interest has this call where the DP=8, but the AD field only shows the reads supporting the REF allele (AD = 7,. ):
GT:DP:SP:AD:SCR:PL:GP:GQ 0/0:8:0:7,.:0:.:.:.
I know that GATK mentions that 'uninformative reads' are not counted when using Haplotypecaller. Am I correct to assume this is the same behavior as in bcftools call and if so, how it considers reads to be uninformative?
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