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DepthOfCoverage (without -L option) output

fulviodanfulviodan ItalyPosts: 3Member

Hi there! I tried to analyse the depth of coverage of my exome data using GATK DepthOfCoverage

java -Xmx${heap}m \
-Djava.io.tmpdir=$processed_bam/tmp_folder_dept \
-jar $gatk \
-T DepthOfCoverage \
-omitBaseOutput \
-omitLocusTable \
-R $GRCh37_ref_WholeGenome \
-I $file \
-o $coverage/${samplename}.coverage.dept
I am not interested in particular genomic regions, so I haven't a target list file. How were the intervals determined in "_interval_statistics" output file? Where can I obtain an interval target list file including all exons in the human genome? Thank you very much!

Fulvio

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