How can I get all variants (.vcf) found in ≤20% of total reads in .bam?
Single-End RNAseq, I have STAR 2-pass aligned .bam files (several samples).
Competed Marked duplicates & sort (Picard), and SplitNCigarReads, BaseRecalibration (GATK)
I generated .vcf (samtool mpileup and BCFTools call) containing number of reads supporting a variant (DP=raw_depth, AD=Total Allelic depth).
My aim is to:
A:get variant.vcf present in ≤20% of total reads in .bam file.
B: detect rare variants.
Is there any program or script available ?
Thanks in advance.