Command-line utilities for processing and analyzing 10X linked-read WGS data
Contact: Ryan Collins (rlcollins@g.harvard.edu)
All code copyright (c) 2017 Ryan Collins and is distributed under terms of the MIT license.
Iterates through a 10X bam file and estimates original molecule lengths and coordinates from colinear reads with matching BX tags (i.e. 10X barcodes).
usage: getMolecules.py [-h] [-d DIST] ibam outfile
Estimate original molecule sizes and coordinates from 10X linked-read WGS
barcodes
positional arguments:
ibam Input bam
outfile Output bed file
optional arguments:
-h, --help show this help message and exit
-d DIST, --dist DIST Molecule partitioning distance in bp (default: 50000)
Usage Notes:
- Input bam file must be coordinate-sorted and indexed.
- "Parititioning distance" (option -d / --dist) is the maximum distance permitted between two colinear reads with matching BX tags before considering them to have arisen from independent molecules.