HsMetrics

= HsMetrics =

from Picard_CalculateHsMetrics

Get header $samtools   view -H    subject.realigned.recal.bam    >    header.txt

Make Bait and Target files m=0 for i in `cat exon.target.interval_list`  ;   \ do echo "$i"; echo "MPMPMP$m"; m=$(($m + 1)) ; \ done > exon.target.interval_list.tmp2

perl -0777 -i -pe "s/\nMPMPMP/\ttarget_/g" exon.target.interval_list.tmp2 perl -0777 -i -pe "s/\r\t/\t/g" exon.target.interval_list.tmp2 perl -0777 -i -pe "s/:/\t/g" exon.target.interval_list.tmp2 perl -0777 -i -pe "s/-/\t/g" exon.target.interval_list.tmp2 cat header.txt exon.target.interval_list.tmp2 >  exon.target.interval_list.picard

Calculates a set of Hybrid Selection specific metrics from an aligned SAMor BAM file. If a reference sequence is provided, AT/GC dropout metrics will be calculated, and the PER_TARGET_COVERAGE option can be used to output GC and mean coverage information for every target.

BAIT_INTERVALS=File	An interval list file that contains the locations of the baits used. Required. TARGET_INTERVALS=File	An interval list file that contains the locations of the targets. Required. INPUT=File	An aligned SAM or BAM file. Required. OUTPUT=File	The output file to write the metrics to. Required. Cannot be used in conjuction with option(s) METRICS_FILE (M) METRICS_FILE=File	Legacy synonym for OUTPUT, should not be used. Required. Cannot be used in conjuction with option(s) OUTPUT (O) METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel	The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list. REFERENCE_SEQUENCE=File	The reference sequence aligned to. Default value: null. PER_TARGET_COVERAGE=File	An optional file to output per target coverage information to. Default value: null. java -Xmx${heap}m -jar ${picard}/CalculateHsMetrics.jar \ BAIT_INTERVALS\=$BaitFilePicard \ TARGET_INTERVALS\=$ExonFilePicard  \ INPUT\=$PWDS/${subjectID}.realigned.recal.bam \ OUTPUT\=$PWDS/${subjectID}.realigned.recal.hsmetrics

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