Question: Extract a list of SNPs from a BCF file
gravatar for Fersal
7 months ago by
Fersal20 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 • 353 views
ADD COMMENTlink modified 7 months ago by genomax63k • written 7 months ago by Fersal20

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 7 months ago by RamRS20k
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