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## Introduction

snpFC - a python tool for filtering and comparing SNPs from multiple VCF files

## Requirement

1) python v3.0+
2) pyvcf

Command line Usage

1) snpfc.py --help

```
usage: snpfc.py [-h] [--vcf VCF [VCF ...]] [--filter] [--compare]
[--frequency FREQUENCY] [--pvalue PVALUE]
[--genotype GENOTYPE] [--quality GENOTYPE_QUALITY]
[--rawreaddepth RAW_READ_DEPTH]
[--qualityreaddepth QUALITY_READ_DEPTH]
[--depthreference DEPTH_IN_REFERENCE]
[--depthvariant DEPTH_IN_VARIANT] [--show] [--outdir OUTDIR]

Script to filter the SNPs using user threshold values and compare the SNPs
from multiple VCF files

optional arguments:
-h, --help show this help message and exit
--vcf VCF [VCF ...] Space separated vcf input files
--filter Filter the SNPs
--compare Compare the SNPs
--frequency FREQUENCY
Frequency of SNP call. Default: 70 [int]
--pvalue PVALUE Pvalue of the SNP call. Default: 0.05 [float]
--genotype GENOTYPE Genotype of the SNP call -
heterozygous/homozygous/both. Default: heterozygous
--quality GENOTYPE_QUALITY
Genotype quality of the SNP call. Default: 10
--rawreaddepth RAW_READ_DEPTH
Raw read depth of the SNP call. Default: 5
--qualityreaddepth QUALITY_READ_DEPTH
Quality read depth of the SNP call. Default: 5
--depthreference DEPTH_IN_REFERENCE
Depth in reference of the SNP call. Default: 5
--depthvariant DEPTH_IN_VARIANT
Depth in variant of the SNP call. Default: 5
--show Display the results on the screen
--outdir OUTDIR Path to the output folder. Default: Current working
directory
```
2) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./
3) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --compare --outdir ./
4) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./ --genotype homozygous --frequency 80
5) python3 scripts/snpfc.py --vcf testfiles/test1.vcf testfiles/test2.vcf testfiles/test3.vcf --filter --outdir ./ --genotype_quality 20

## Usage as python module
### usage of filter module
```
import snpfc
from snpfc.snpFilter import snpfilter
dofilter = snpfilter(input.vcf, output.vcf, frequency=70, pvalue=0.05, genotype='any', genotype_quality=20, raw_read_depth=5, quality_read_depth=5, depth_in_reference=5, depth_in_variant=5)
dofilter.filter()
```
This will filter the SNPs and save in output.vcf file.

### usage of compare module

```
from snpCompare import snpcompare
docompare = snpcompare([input1.vcf, input2.vcf, input3.vcf]) # takes array of input files
docompare.compare()

```

This will compare the SNPs in the input files and save the output in the files - input1_snpcompare.txt, input2_snpcompare.txt and input3_snpcompare.txt in the current working directory.

```
docompare.compare(output_directory)
```

This will save the output files in the output directory specified.


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