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)

hsmetrics

Format

cg hsmetrics ?options? bamfile targetfile resultfile

Summary

Creates a hsmetrics file using picard CalculateHsMetrics

Description

This command makes the use of picard CalculateHsMetrics to calculates a set of Hybrid Selection specific metrics from an aligned BAM file a bit easier by autoconverting some of the input files, and adding a sample column. It does not support all the options of picard.

Arguments

bamfile: bamfile
targetfile: tsv region file containing the target regions
resultfile: name of reulting file

Options

-s sample (--sample): Give the name of the sample. If not given, it the name will be deduced from the bam filename
-b baitfile (--baitfile): tsv region file containing the bait regions. If not given, the target regions will also be used as bait regions.

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