Computes additional coverage statistics downstream of GATK's DepthOfCoverage.
usage: Run additional coverage statistics for a single case.
[-h] [-b BASEPATH] [-m MEDGAPDIR] [-q QCDIR] [-d DBASESDIR]
[-t TOOLSDIR] [--case CASE] [--fullqcdir FULLQCDIR]
optional arguments:
-h, --help show this help message and exit
-b BASEPATH, --basepath BASEPATH
path to "cases" directory (default: /srv/gsfs0/SCGS)
-m MEDGAPDIR, --medgapdir MEDGAPDIR
MedGap subdirectory, relative to basepath (default:
latest)
-q QCDIR, --qcdir QCDIR
QC subdirectory, relative to medgapdir (default:
latest)
-d DBASESDIR, --dbasesdir DBASESDIR
genelists subdirectory, relative to basepath (default:
pipeline/dbases/0.2)
-t TOOLSDIR, --toolsdir TOOLSDIR
tools subdirectory, relative to basepath (default:
pipeline/coverage_stats/0.2)
--case CASE name of case subdirectory (for example, case0017)
(default: None)
--fullqcdir FULLQCDIR
Full path to QC directory. If provided, overrides
basepath, medgapdir, qcdir, and case. (default: None)
For example:
./coverage_stats.py case0011
Notes:
Stderr and stdout files from qsub are placed in user's home directory. This matches the behavior of the original scripts.
Overview of scripts:
add_genes_qsub.pl, calls add_exonname_coverage.pl on each chromosome Input: $TYPE_coverage_hist_$Q.txt Output: $TYPE_coverage_hist_$Q_withgenes_$chr.txt, $TYPE_coverage_hist_$Q.txt_$chromosome_$thresholds.stat
compute_gene_stats.pl Input: coverage directory path Output: refseq_exon_stats_$Q.txt
grab_genes_stats.pl Input: refseq_exon_stats_$Q.txt, gene list Output: $panel_exon_stats_$Q.txt
query_stats.pl input: $panel_exon_stats_$Q.txt output: $panel_exon_stats_$Q.txt.query.out
collect_stats.pl Input: $panel_exon_stats_$Q.txt Output: $panel_coverage_stats_min$thr[$i].txt
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