Efficient variant caller for next generation sequencing (NGS) data
fastVariant infers variants from a bam file and outputs them in a variant call format (.vcf file).
By running python main.py -h you can see the expected input format.
usage: main.py [-h] --genome GENOME --sam SAM [SAM ...] [--bed BED] --rname
RNAME --vcf VCF
Computational Biomedicine Ex 2
optional arguments:
-h, --help show this help message and exit
--genome GENOME Path to reference genome
--sam SAM [SAM ...] Path to SAM files. If using more than one separate
using a space
--bed BED Path to BED file
--rname RNAME Reference name of genome so that SAM file can be
filtered. Ex, use chr22 for chromosome22
--vcf VCF Path to VCF output file
An example of running command is:
python main.py --genome data/genome.chr22.fa --bed data/bed_chr_22.bed --sam data/alignedreads.sam --rname 'chr22' --vcf output.vcf