variant filtering

Question

[milad]

Hello How and with what scripts can I apply the following filters in a file that includes all variants of the genome? Please explain in detail

i want remove Variants with phred-scaled scores below 20 and variants with genotypic qualities (GQ) of less than 20, SNPs within 5 bp of an indel, indels within 10 bp of each other, variants with a depth of coverage below 33% or more than twice mean genome coverage of the alignment

[Pierre Lindenbaum]

with phred-scaled scores below 20 and variants with genotypic qualities (GQ) of less than 20, SNPs

bcftools view with option -i. See the manual.

, SNPs within 5 bp of an indel, indels within 10 bp of each other,

I think, you'll need programming...

[jeevii]

Hello, you can go with bcftools- vcfutils.pl varFilter options to filter.

https://github.com/samtools/bcftools/issues/30