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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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Add 10X processing mode. #33

Closed constantAmateur closed 6 years ago

constantAmateur commented 6 years ago

I wrote this modification in order to handle a specific requirement I had to count allele frequencies in 10X single cell RNA-seq data. The vendors processing pipeline (cellranger) produces a BAM file which has special tags indicating which droplet a read is from (the cellular barcode) and which molecule it was generated from (the UMI).

This code will count the number of UMIs supporting each allele at each specified location, for each cellular barcode present at that location. Because there are multiple reads per UMI, a consensus allele for each molecule is calculated.

I wrapped this behaviour within separate statements that are enabled with the -x flag. In order to get the desired output in 10X mode, I moved the printing to file into the bam_access.c routines.

keiranmraine commented 6 years ago

Merged into a different branch