Loop using BCFTOOLS ?

Question

[rotemkat]

Hi!

I have a list of mutations, and I want to know which of them are germline mutations and appear in the dbSNP (I downloaded the VCF file). Is there an efficient way to run over this list using bcftools, rather than going line by line and filter the dbSNP accordingly?

Thanks!!

[rotemkat]

Hi, Thanks! Still having problem, can you elaborate a bit? Also, can I use the second list as csv/xlsx file? or i have to find a way to convert it to vcf file?

Thanks!!!

[Pierre Lindenbaum]

you have to tell use what you are doing, what the commands you used.

[rotemkat]

I think part of my problem is because the list of mutations is not in a vcf file, but just txt file. I tried to save it as vcf and tried the following commands:

./bcftools isec -p myList.vcf.gz dbSNP.vcf.gz ---> Expected multiple files or the --targets option

./bcftools isec -C /myList.vcf.gz dbSNP.vcf.gz ---> Failed to open myFile.vcf.gz: unknown file type

./bcftools isec -c both -p myList.vcf.gz dbSNP.vcf.gz ---> Expected multiple files or the --targets option

./bcftools isec -c both -p path myList.vcf.gz dbSNP.vcf.gz ---> Failed to open myList.vcf.gz: unknown file type

Answer 1

[Pierre Lindenbaum]

'bcftools view' with option '--regions-file'....

and then bcftools isec with dbsnp