Tools for filtering SNPs near indels in VCF files

Question

[falconblue]

Hi, all,

I have files containing SNPs and indels of the same samples in the VCF format. How can I find the right tools to filterSNPs near indels? I have tried the Varscan filter program, but I can't change parameters in it. Thank you!

Answer 1

[iraun]

You can try bcftools filter with -g, --SnpGap argument which filters SNPs within INT base pairs of an indel.
For ore information here is the manual link: https://samtools.github.io/bcftools/bcftools.html#filter.

Hope it helps.