ShujiaHuang / basevar

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

BaseVar

This is the official development repository for BaseVar, which call variants for ultra low-pass (<1.0x) WGS data, especially for NIPT data.

Prerequisites

BaseVar requires HTSlib 1.3(or later) and Cython. You should compile htslib and install Cython before build BaseVar.

pip install cython

HTSlib can be downloaded from the htslib web site.

To compile and install HTSlib, cd into HTSlib source and type make install. This will install HTSlib under /usr/local/ (see note below). To install HTSlib in any other directory use make install prefix=/path/to/dir.

NOTE: HTSlib should be installed in a standard location (e.g. /usr/local/).

If not installed in a standard location, you will need to set your library paths:

For GNU/Linux

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib
export LD_LIBRARY_PATH=/path/to/dir/lib

Note the /include and /lib sub-directories. e.g. if you installed HTSlib under /Users/me/htslib then set

export C_INCLUDE_PATH=/Users/me/htslib/include
export LIBRARY_PATH=/Users/me/htslib/lib
export LD_LIBRARY_PATH=/Users/me/htslib/lib

HTSlib will automatically make the include and lib directories on install.

For OSX

export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib
export DYLD_FALLBACK_LIBRARY_PATH=/path/to/dir/lib

Installation

To build BaseVar, please download the stable version which is v0.8.0, do the following:

wget https://github.com/ShujiaHuang/basevar/archive/v0.8.0.tar.gz

Then do

$ tar zxvf v0.8.0.tar.gz
$ cd basevar-0.8.0/
$ python setup.py install

Now you can use basevar in your commandline.

Quick start

Call variants from several bamfiles

basevar basetype -R reference.fasta \
    --regions chr11:5246595-5248428,chr17:41197764-41276135 \
    --batch-count 50 \
    -I 00alzqq6jw.bam \
    -I 09t3r9n2rg.bam \
    -I 0fkpl1p55b.bam \
    -I 13dg1gvsfk.bam \
    -I 17phildszl.bam \
    -I 1dbpgqt0dq.bam \
    -I 1kyws27hoc.bam \
    --output-vcf test.vcf.gz \
    --output-cvg test.cvg.tsv.gz \
    --nCPU 4 && echo "** job done **"

Or call variants from bamlist

basevar basetype -R reference.fasta \
    --regions chr11:5246595-5248428,chr17:41197764-41276135 \
    --batch-count 50 \
    -L bamfile.list \
    --output-vcf test.vcf.gz \
    --output-cvg test.cvg.tsv.gz \
    --nCPU 4 && echo "** job done **"