Local.md

Local Installation

1. Tool Prerequisites

• python=3.7
• samtools and bcftools

    git clone --branch=develop git://github.com/samtools/htslib.git
    git clone --branch=develop git://github.com/samtools/bcftools.git
    git clone --branch=develop git://github.com/samtools/samtools.git
    cd bcftools; make
    cd ../samtools; make 

• PyVCF

pip3 install PyVCF

• pandas

pip3 install pandas

• snakemake

pip3 install snakemake

2. Clone cfCloud

git clone https://github.com/NHLBI-BCB/cfCloud.git
cd cfCloud

3. Install resources

• Bowtie2 Reference Genome
  Can be downloaded from Illumina iGenomes

# e.g. hg19:
cd resources
wget http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
tar -xzf Homo_sapiens_UCSC_hg19.tar.gz

• SNPs list
  Can be downloaded from Illumina Genotyping Kits

# e.g. Infinium Omni2.5:
cd reources
unzip InfiniumOmni25.hg19.snps.cleaned.zip

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