Filtering SNPs by coverage in HapMap format

[Nick Bell]

I have data GBS derived from the UNEAK pipeline and I'd like to use the count.hmc file to remove SNPs from my HapMap.hmn file which fall below a given threshold (i.e. 20x).

I've done a fair bit of looking around and have not found a straightforward way to do this quality control.

Any suggestions of how to do this? It seems strange that the depth of coverage data is segregated from the rest of the data in the first place.

[TiborNagy]

If your pipeline can make VCF output, please use it. This format contains your SNPs, coverage information and many other useful informations. Filtering VCFs is also easy with vcftools.

[Nick Bell]

It is possible that that is an option. I'm entirely new to NGS and bioinformatics.
I will have to look into that.

[arthurmelo]

look this examples in vcftools ...

http://vcftools.sourceforge.net/perl_examples.html