Using bed file to identify callable sites

[juanitagutierrez]

Hi :)

I would like to understand how to use the bed file produced by gimbleprep to reproduce the VCF generated by gimble after this first step. It seems like the bed file lists all loci, e.g.,

chr1 0 137 10 sample_1,sample2,sample3,...,sample10
chr1 137 139 11 sample_1,sample2,sample3,...,sample11
chr1 139 169 10 sample_1,sample2,sample3,...,sample10
chr1 169 177 11 sample_1,sample2,sample3,...,sample11
chr1 177 180 12 sample_1,sample2,sample3,...,sample12

Should one pre-filter the bed file to keep only sites supported by more than N samples?
Thanks in advance for your help.

Best,