diff --git a/README.md b/README.md index 82c0449..9471063 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,12 @@ # VarGeno Fase SNP genotyping tool for whole genome sequencing data and large SNP database. -# Prerequisites -- A modern, C++11 ready compiler, such as `g++` version 4.9 or higher. -- The cmake build system (*only necessary to install SDSL library. If SDSL library already installed, cmake is not needed*) -- A 64-bit operating system. Either Mac OS X or Linux are currently supported. +# Install from Bioconda +VarGeno can be installed from Bioconda with command `conda install vargeno`. -# Quick Install -``` -git clone https://github.com/medvedevgroup/vargeno.git -cd vargeno -export PREFIX=$HOME -bash ./install.sh -``` -You should then see `vargeno` in vargeno directory. To verify that your installation is correct, you can run the toy example below. +Go to [this link](https://bioconda.github.io/#using-bioconda) for more information about Bioconda. + +If you do not have Bioconda installed, you can [install VarGeno from source code](#install-from-source-code). # Quick Usage @@ -43,23 +36,38 @@ VarGeno's genotyping results are in the "FORMAT" column of VCF file. For details of "GT" and "GQ" fields, please refer to [The Variant Call Format(VCF) Version 4.2 Specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf). -# Example +# Install from Source Code -In this example, we genotype 100 SNPs on human chromosome 22 with a small subset of 1000 Genome Project Illumina sequencing reads. The whole process should finish in around a minute and requries 34 GB RAM. Suppose VarGeno is installed in directory `$VARGENO`. +### Prerequisites +- A modern, C++11 ready compiler, such as `g++` version 4.9 or higher. +- The cmake build system (*only necessary to install SDSL library. If SDSL library already installed, cmake is not needed*) +- A 64-bit operating system. Either Mac OS X or Linux are currently supported. -1. go to test data directory +### Install Command ``` -cd $VARGENO/test +git clone https://github.com/medvedevgroup/vargeno.git +cd vargeno +export PREFIX=$HOME +bash ./install.sh ``` +You should then see `vargeno` in vargeno directory. To verify that your installation is correct, you can run the toy example below. + +# Example + +The example dataset is in [https://github.com/medvedevgroup/vargeno/tree/master/test](https://github.com/medvedevgroup/vargeno/tree/master/test) . + +In this example, we genotype 100 SNPs on human chromosome 22 with a small subset of 1000 Genome Project Illumina sequencing reads. The whole process should finish in around a minute and requries 34 GB RAM. + +1. go to test data directory 2. pre-process the reference and SNP list to generate indices: ``` -$VARGENO/vargeno index chr22.fa snp.vcf test_prefix +vargeno index chr22.fa snp.vcf test_prefix ``` 3. genotype variants: ``` -$VARGENO/vargeno geno test_prefix reads.fq snp.vcf genotyped.vcf +vargeno geno test_prefix reads.fq snp.vcf genotyped.vcf ``` # Memory Lite Version