Loop using BCFTOOLS ?
1
0
Entering edit mode
21 months ago
rotemkat ▴ 10

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!!

bcftools dbsnp • 575 views
ADD COMMENT
0
Entering edit mode

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!!!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
21 months ago

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

and then bcftools isec with dbsnp

ADD COMMENT

Login before adding your answer.

Traffic: 1852 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6