Sambamba depth tools does not report softclipped bases

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

GNU General Public License v2.0

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Sambamba depth tools does not report softclipped bases #457

Closed robinpaul85 closed 3 years ago

robinpaul85 commented 3 years ago

I noticed that the sambamba depth tool does not report the number of soft clipped bases. Can it report the number of softclipped bases ? I noticed that the "REFSKIP" column is always empty? What is that column for? I am using sambamba 0.7.1.