mapmygenome filter on GC.Score

[satishmp]

The mapmygenome file has additional column GC.score, that gives the confidence level of the SNP.
It will be good to filer out SNP rows that has lower confidence (say < 0.75).

Requesting for adding this feature of filtering rows based on GC.score into your module.

[apriha]

Thanks for the suggestion @satishmp .

@willgdjones , do you know if this is the GenCall score? Per that paper (under "GenCall Score Cutoff"), it looks like SNPs with GenCall scores <0.15 aren't called, and a threshold of 0.15 is considered standard.

So, if GC.score is GenCall score, I could see adding it as a convenience to filter out SNPs (i.e., set genotype to null) if Mapmygenome calls SNPs when the score is <0.15. Do either of you know if this happens?

[willgdjones]

I'm not 100% sure. Tagging @afaulconbridge here too!