Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
DepthOfCoverage for whole genome: skipped few regions
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.