GenomeComb
Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)
cg predictgender ?options? bamfile/sampledir ?outfile?
predicts gender for a sample
cg predictgender calculates a number of relevant metrics and predicts the gender of the given sample. It outputs the results in report form (tsv file with parameter/value fields). The predicted gender is in the predgender line in the results.
Usually the sampledir is given as argument, and the command will find all files needed for the prediction in it. If a bamfile is given instead, the command will look for other files needed in the same directory. The other files used can however also be given explicitely using options (-varfile, -targetfile)
The measures compare the non-pseudoautosomal region on the Y chromosome (yreg) to the non-pseudoautosomal region on the X chromosome (xreg). these regions can be derived from data in the given reference dbdir (-dbdir) or given directly by the options -regy and -regx.
The gender prediction is primarily based on the the ratio of median coverage of 500 target regions in regy vs regx (pg_yxcovratio). If this is unclear (insufficient X coverage, between 0.1 and 0.3), a combination of the ratio of number of reads mapping to regy (normalized vs the target region) vs that of regx (pg_yxnratio), and the percentage of heterozygous high quality variants (pg_pcthqheterozygous) is used.
Report