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.

Pre-requisites

Assuming you have python3 already, install pyVCF

pip install pyvcf

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

Indices and tables