Question: number of snps in the bgen file (snptest)
1
gravatar for muralinmars
5.1 years ago by
muralinmars80
France
muralinmars80 wrote:

Hi,

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

Thanks

 

snptest snp • 2.0k views
ADD COMMENTlink modified 2.7 years ago by gavinband20 • written 5.1 years ago by muralinmars80

Thanks,

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

ADD REPLYlink modified 12 months ago by RamRS30k • written 5.1 years ago by muralinmars80
1
gravatar for gavinband
2.7 years 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 2.7 years ago by gavinband20
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