Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
Conbase is a software for identification of somatic mutations in single cell DNA sequencing data exhibiting high rates of allelic dropout and at low read depth. Conbase leverages data from multiple samples in a dataset, and utilizes read phasing to call somatic single nucleotide variants and to accurately predict genotypes in whole genome amplified single cells.
Algorithm developed by Ezeddin Al Hakim, Marie Kindblom & Joanna Hård.
Stats.py:
python3 bin/Main.py stats <snp path> <bam path> <reference path> <number of nodes> <output name>
Analyze.py:
python3 bin/Main.py analyze <json path> <output name>
input format bam file
NAME PATH
cell1 data/cell1.bam
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input format snp file
CHROM POS REF ALT
1 23142496 C A
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- Marie Kindblom - (https://github.com/mkindblom)
- Ezeddin Al Hakim - (https://github.com/ezeddin)
This project is licensed under the MIT License - see the LICENSE.md file for details