number of snps in the bgen file (snptest)

Question

[muralinmars]

Hi,

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

Thanks

[muralinmars]

Thanks,

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

Answer 1

[gavinband]

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.