RCollins13 / 10XWGS

Utilities for processing 10X linked-read WGS data

10XWGS

Command-line utilities for processing and analyzing 10X linked-read WGS data

Contact: Ryan Collins ([e-mail])

All code copyright (c) 2017 Ryan Collins and is distributed under terms of the MIT license.

getMolecules.py

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:

1. Input bam file must be coordinate-sorted and indexed.
2. "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.