Question: Tools for filtering SNPs near indels in VCF files
1
gravatar for falconblue
3.9 years ago by
falconblue10
China
falconblue10 wrote:

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! 

snp • 1.6k views
ADD COMMENTlink modified 3.9 years ago by iraun3.5k • written 3.9 years ago by falconblue10
3
gravatar for iraun
3.9 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

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.

ADD COMMENTlink written 3.9 years ago by iraun3.5k
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