Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

DepthOfCoverage for whole genome: skipped few regions

NeelamNeelam Posts: 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.


Best Answers


Sign In or Register to comment.