Question: number of snps in the bgen file (snptest)
1
gravatar for muralinmars
4.2 years ago by
muralinmars70
France
muralinmars70 wrote:

Hi,

Is there a way to know the number of snps in the bgen file for each of the chromosome.

Thanks

 

snptest snp • 1.5k views
ADD COMMENTlink modified 22 months ago by gavinband20 • written 4.2 years ago by muralinmars70

Thanks,

Used qctool to get a summary_stats and know the number of SNPs.

ADD REPLYlink modified 8 weeks ago by RamRS25k • written 4.2 years ago by muralinmars70
1
gravatar for gavinband
22 months ago by
gavinband20
gavinband20 wrote:

Here are two other ways:

1: Using qctool: running qctool -g myfile.bgen [1] prints out a summary of the input data, including the number of variants and samples in the file.

2: Using bgenix: E.g. the command bgenix -g myfile.bgen -incl-range 22:0- -list would list all variants on chromosome 22. (You might have to index the file with bgenix -g myfile.bgen -index first.)

Best, g.

ADD COMMENTlink written 22 months ago by gavinband20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1031 users visited in the last hour