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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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Indel support #50

Closed ibwoo closed 5 years ago

ibwoo commented 5 years ago

Is it possible that this tool will ever offer support for counting indels?

AndyMenzies commented 5 years ago

No, thats not what this tool is for. AlleleCount will tell you how many times A, C, G and T are seen at specified single point locations within a bam file. Accurate counting of indels usually involves remapping reads, and that is outside of the scope of this application.

If you are interested in indel detection we have cgpPindel