Hi all
I am using samtools mpileup for variant calling but bit confused with using -D for maximum read depth to call variants.
As my understanding, the minimum coverage (like "-d" in this tool) is normally used for variant calling as the threshold but this case is for the maximum depth. Thus, the way I used for my exome sequencing is
Is there any recommended read depth setup for variant calling in exome sequencing?
Thanks
I am using samtools mpileup for variant calling but bit confused with using -D for maximum read depth to call variants.
vcfutils.pl varFilter -D100 > var.flt.vcf
vcfutils.pl varFilter -d30 -D1000 > var.flt.vcf
Thanks