Hi, I am trying to use "bcftools isec" for some data analysis. I have two cell lines and I am trying to find the unique mutations in each when compared to the human reference genome. The command I have been using is as follows
bcftools isec "a.vcf.gz" "b.vcf.gz" -C -p dir
This works well, but it stripped all the mutation annotations I had. Allele frequencies, genes, etc. It also outputs the unique mutations as a text tile.
- Is there a way to get use bcftools isec w/o stripping annotations?
- Is there a way to get bcftools isec to output the new file as a VCF file? I would still like to be able to use my data with visualization software such as IGV.
- If either of these does not work, is there some way I can turn a text file into a VCF file? AND is there any way to add mutaion annotations to a text file instead of a VCF file.
Thanks for the help!