How to filter SNP and INDEL separately for VCF files
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Entering edit mode
10 weeks ago
Yiming ▴ 10

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!

VCF filter • 202 views
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2
Entering edit mode
10 weeks ago

use bcftools concat to merge both files.

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