VCF_parser

Generates chromosome arm information using VCF and cytoband files

Dependencies: Requires installation of pyvcf, A Variant Call Format Parser for Python

Install as follows: pip3 install pycvf

See requirements.txt for the other packages used in the code

Run the script as follows: python3 main.py [-i INFILE [INFILE ...]] [-c CYTOBAND] [-o OUTFILE]

Example command: python3 main.py -i CN_segments.vcf -c ../cytoBand.txt -o cytoband_out.tsv

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
.ipynb_checkpoints		.ipynb_checkpoints
src		src
3-23965487.C-2_TVQCSS5_5DR7E_5DR7E.tsv		3-23965487.C-2_TVQCSS5_5DR7E_5DR7E.tsv
3-23966692.C-2_TVQCSS5_5DR7E_5DR7E.tsv		3-23966692.C-2_TVQCSS5_5DR7E_5DR7E.tsv
3-23966692.C-2_TVQCSS5_5DR7E_5DR7E_mosaic.tsv		3-23966692.C-2_TVQCSS5_5DR7E_5DR7E_mosaic.tsv
CO221981-1_cytoband.tsv		CO221981-1_cytoband.tsv
README.md		README.md
cytoBand.txt		cytoBand.txt
main.py		main.py
requirements.txt		requirements.txt

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