Tools for filtering SNPs near indels in VCF files
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!
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falconblue •
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1 answer
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.
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