SNPcallPipe

Pipeline to call snps using a reference genome

Download

    git clone https://github.com/Yuma248/SNPcallingPipe

Dependecies

Perl Parallel:::Loops

GNU Parallel

Stacks

AdapterRemoval

Bowtie2

BWA

SNAP

samtools

bcftools

vcftools

The easiest way to install the dependencies is using conda

conda create --name SNPcallPipe -c conda-forge -c bioconda perl-parallel-loops parallel stacks adapterremoval bowtie2 bwa samtools bcftools vcftools

For SNAP

    git clone https://github.com/amplab/snap.git

    cd snap

    make 

Then copy snap-aligment to your path or incluide snap folder in your $PATH

Basic usage:

Usage:

SNPcallPipe

    -stp <You need at least determine what steps you want to run>
    
            indref: <Indexs the reference genome with samtools, picard, bowtie2 and snap>
            
            demul: <It will use stacks process_rad script, to demultiples samples base on a barcode file>
            
            trim: <It will use AdapterRemoval to trim and filter reads>
            
            aligment: <It will use bowtie2, bwa or snap to align reads to a referecne genome>
            
            dedup: <This step will sort sam files, cnvert to bam and mask duplicates>
            
            indelrea: <This step will locally realign indels, although this is not recomended any more>
            
            calling: <This step will use bcftool and mpileup to call variant sites SNP/indel>
            
            filtering: <This step will use vcftools to filter SNPs, I recomend to use this automatically to have an idea of youdata, but play wiht the parameters if you have the time>