Call variants for ultra low-pass (<1.0x) WGS data, especially for NIPT data.
BaseVar requires HTSlib 1.3(or later) and Cython. You should install Cython before build BaseVar.
pip install cythonHTSlib 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:
export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib
export LD_LIBRARY_PATH=/path/to/dir/libNote 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/libHTSlib will automatically make the include and lib directories on install.
export C_INCLUDE_PATH=/path/to/dir/include
export LIBRARY_PATH=/path/to/dir/lib
export DYLD_FALLBACK_LIBRARY_PATH=/path/to/dir/libTo build BaseVar, do the following:
git clone https://github.com/ShujiaHuang/basevar.gitThen do
$ cd basevar
$ python setup.py installNow you can use basevar in your commandline.
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 **"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 **"