Welcome to documentation of snpFC¶
Introduction¶
snpFC - a python tool for filtering and comparing SNPs from two or multiple VCF files.
How can I get it¶
At the moment, latest snpFC tool can be obtained from github repo link . Just clone the repository or download as a compressed file.
I have a target to upload snpFC to python repository enabling to install using pip command.
Quick Start¶
If you don’t have patience, here is how to run snpFC
python scripts/filter_and_comparesnps.py --vcf testfiles/test1.vcf testfiles/test2.vcf --filter --compare --show --frequency 70 --pvalue 0.05 --genotype heterozygous --quality 10 --rawreaddepth 5 --qualityreaddepth 5 --depthreference 5 --depthvariant 5 --outdir ./testfiles
The above command will output as following
Common and Unique SNPS in vcf File : testfiles/test1.vcf
tig00000003 775 A G common
tig00000003 776 T C common
tig00000003 836 G C unique
tig00000004 1166 G A common
tig00000004 1190 G A unique
Common and Unique SNPS in vcf File : testfiles/test2.vcf
tig00000003 775 A G common
tig00000003 776 T C common
tig00000003 836 G T unique
tig00000004 1166 G A common
tig00000004 1190 G A,C unique
The outputs are saved in these files : /home/shrestha/Sites/test1_snpanalysis.txt /home/shrestha/Sites/test2_snpanalysis.txt
Options¶
Available options:
--vcf space separated two or more vcf files
--filter filter snps
--compare compare snps between vcf files
--frequency frequency threshold value to filter (default: 70)
--pvalue pvalue threshold value to filter ( default: 0.05)
--genotype genotype to filter (default: heterozygous)
--quality genotype quality threshold to filter (default: 10)
--rawreaddepth raw read depth threshold to filter (default: 5)
--qualityreaddepth quality read depth threshold to filter (default:5)
--depthreference depth in reference threshold to filter (default:5)
--depthvariant depth in variant threshold to filter (default:5)
--show show the compared snps on screen
--outdir output directory
To check the options:
python scripts/filter_and_comparesnps.py --help