DepthOfCoverage for whole genome: skipped few regions

NeelamNeelam BlacksburgPosts: 6Member

I used following command to get coverage data for entire genome: java -Xmx2g -jar ~/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -T DepthOfCoverage -R ~/Gmax_189.fa -o DoCov_dedup -I dedup.bam.list

Coverage was not reported for 36025109 bases. Many skipped bases fall one after another in the genome to form big continuous regions. I do not understand, why these regions were skipped. Usually if there was no mapping, the coverage value should be reported as 0.

Appreciate some insight into this issue! Thank you.

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