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.
Category
Report