What's the best way to limit variant calls from amplicon sequencing to desired target regions: Fastq trimming, soft clipping bam files or filtering vcf files?
- Fastq trimming with amplicon primer sequences can take a long time (for large panels like CCP) and requires the primer sequences
- Are there any tools that can soft clip bam files based on target regions?
- Filtering vcf files seems to be the easiest option, but I imagine that upstream modifications will have an influence on downstream variant calls.
This seems like it should be a solved problem, but I couldn't find a clear solution in my internet/biostars search.