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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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AlleleCounter bahavior with soft-clipped reads #64

Open DominikGlodzik opened 4 years ago

DominikGlodzik commented 4 years ago

Hello CancerIT Team,

could you confirm if soft-clipped reads are taken into account in pile-up calculations?

Best wishes Dominik

keiranmraine commented 4 years ago

If a portion of a read is soft-clipped it cannot be considered during counting if that portion is overlapping as it is not considered mapped. @davidrajones may be able to provide further confirmation on this.