BaseVar

Call variants for ultra low-pass WGS data.

Installation

pip install basevar

Prerequisites

BaseVar requires HTSlib 1.3 or greater. HTSlib can be downloaded from the htslib web site.

To build 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

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 "** 5 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 "** 5 done **"

Archieyoung/basevar