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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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Running aC on scRNA BAMs (10X or otherwise) #61

Closed nansari-pour closed 4 years ago

nansari-pour commented 4 years ago

Hi there, Is is essential for the HTS file to be paired-end for aC to work? Specifically, aC only gives 0 counts (and 0 depth) when supplied with an scRNA BAM file. Is there any way around this? Thanks

keiranmraine commented 4 years ago

Not too clear what you are after here. By aC do you mean alleleCounter?

Allele counter acts on a single BAM/CRAM file. All values being 0 is more likely to be due to the input loci BED file (--loci-file) being for the incorrect genome build (chr vs no chr prefix).

ghost commented 4 years ago

I would add that it may be due to default flag filtering. See -f --required-flag and -F --filtered-flag options and select an appropriate value for your data. I find this site useful for working out flag values.

nansari-pour commented 4 years ago

Dear Keiran and David,

1) I am aware of the requirement for matching genome build but the problem is definitely not the chromosome prefix/annotation.

2) the flag option worked beautifully!

Many thanks for your advice and the provided link.

ghost commented 4 years ago

@nansari-pour Glad we could get it working for you.