How to filter SNP and INDEL separately for VCF files

Question

[YL]

Hello,

I have annotated VCF files and I wonder how I can SNP and INDEL separately for VCF files?

For example,

"Keep variants if Fisher’s strand bias score (FS) less than 200 (INDELs) or less than 60 (SNPs)"

I have been thinking about filtering SNP and INDEL to create two separate VCFs (such as "bcftools view -i 'FS < 60' sample.vcf --types snps" and "bcftools view -i 'FS < 200' sample.vcf --types indels). But I am not sure how to merge the two files from the SAME sample.

Thank you very much for the help!

Answer 1

[Pierre Lindenbaum]

use bcftools concat to merge both files.