Depth of coverage

= Depth of coverage = Determine coverage summarized by mean, median, quartiles, and/or percentage of bases covered. Make a temp directory mkdir -p ${tmp_folder}_dept Running GATK depth of coverage java -Xmx${heap}m -Djava.io.tmpdir\=${tmp_folder}_dept \ -jar $gatk \ -T DepthOfCoverage \ -L $ExonFile \ -l INFO \ -R $REF \ -I $PWDS/${subjectID}.realigned.recal.bam \ -o $PWDS/${subjectID}.coverage.dept \ -L $ExonFile

Remove the temp directory

rm -rf ${tmp_folder}_dept

Make a coverage directory and move all output to this folder mkdir -p $PWDS/coverage mv $PWDS/${subjectID}.coverage.dept* $PWDS/coverage/

Calculate coverage for all subjects for i in `cat list.txt` do

echo -ne "$i\t" >> coverage.txt

cat ../$i/analysis/coverage_normdup/$i.coverage_normdup.dept.sample_cumulative_coverage_proportions  \ | cut -f 8,10,12,22 >> coverage.txt cat ../$i/analysis/coverage/$i.coverage.dept.sample_cumulative_coverage_proportions  \ | cut -f 8,10,12,22 >> coverage.txt

done

perl -0777 -i -pe "s/\ngte_6\tgte_8\tgte_10\tgte_20\n/\t/g" coverage.txt perl -0777 -i -pe "s/gte_6\tgte_8\tgte_10\tgte_20\n//g" coverage.txt

mv coverage.txt tmp1 cat tmp1 | sort -k 2 -n -r > coverage.txt rm -f tmp1

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