Question: Extract a list of SNPs from a BCF file
gravatar for Famf
12 months ago by
United States
Famf20 wrote:

Hi there, I have a very large BCF file from which I want to extract a list of SNPs (also very large). The SNPs of interest are in a tab delimited file with two columns chromosome and position. I have tried the bcftools by using view function and the options -T and -R like bellow but I haven't had success.

bcftools view -T mylist.txt file.bcf -Ou -o filteredfile.bcf

Thanks in advance

snp bcf • 577 views
ADD COMMENTlink modified 12 months ago by genomax70k • written 12 months ago by Famf20

but I haven't had success

What does that mean? What is the exact problem you're facing? Can you also paste the first few lines of your mylist.txt file?

ADD REPLYlink written 12 months ago by RamRS23k
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