Alignment reads: parent-of-origin filtering

Filter out parent-of-origin alignment reads according to SNP databases.

Install

filter_reads.py requires pysam library.

You can install pysam:

sudo yum install python-pip
pip install pysam

Usage

filter_reads.py in.sam snp1.csv snp2.csv

SNP data files *.csv have the following format:

chr,pos,ref,alt
1,3000248,G,T
1,3000289,T,G
1,3000353,C,T
1,3000355,T,C
1,3000444,T,A
1,3000906,G,T

chr: chrome name without chr prefix pos: SNP position ref: Reference base alt: Alternative base

*.mup files

*.mup files illustrate the underlying algorithms the script uses, they can be opened with https://www.mindmup.com an on-line mind storm editor.