Need help! Sifting through mutations in other cell lines (parameters and tools)

[mggrami]

Hi!

I am looking for mutations (snp, indels ...) before and after cultivation in cancerous cell lines.

However I am not sure how can i set up parameters to omit mutations in hg.38, and additionally mutations in healthy PBMC.

I got three short reads data sets (before after and PBMC all in fasta) and i would like to obtain:

mutations private to cell lines before cultivation - hg.38 mutations - PBMC

mutations private to cell lines after cultivation - hg.38 mutations - PBMC

and common mutations for both cell lines after and before cultivation - hg.38 mutations - PBMC

Previously I was doing it utilizing bcftools isec (working on vcf files)

Is there a way to do this in one command in one sample sheet? What programs shall I use?

Sincerely,
Michał