Integrate read end clipping in to allelecounter

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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Integrate read end clipping in to allelecounter #60

Open danchubb opened 4 years ago

danchubb commented 4 years ago

alleleCount-FixVAF is a fork which includes a "-e n" parameter which ignores all sites within n bases of the end of the read.

This is to correct an issue with reference bias in the illumina Isaac aligner described in https://www.biorxiv.org/search/chubb%252Bcornish

The default -e is 5. Might be worth changing it to 0 if it was to be rolled in to the main allelecounter.