Fuwa

A decision-tree-based fast variant caller.

Install

You can directly download the complete package using the following command:

wget -c http://rubywu.cn/public/fuwa.tar.gz

and then

tar zxvf fuwa.tar.gz
cd fuwa
sh install.sh
# Test Fuwa with sim data
sh test.sh

Alternatively, you can clone this repository to your computer and make the executable file.

The reference files and the gziped dbSNP file can be downloaded using the following commands:

# reference
wget -c http://rubywu.cn/public/reference.tar.bz2
# dbSNP
wget -c http://rubywu.cn/public/dbsnp141.gz

Attention: A 64-bit Linux OS is required for make. Type getconf LONG_BIT to see your OS bits.

Usage:

fuwa [options]
-i input     input bam file
-d dbSNP     dbSNP gz file
-r ref_dir   reference directory
-o output    [optional] output file name without extension (default: input file name)
-s SNP_qual  [optional] Filtering threshold of quality score for SNPs (range: [0, 1], default: 0.8)
-q qual      [optional] Filtering threshold of quality score for indels (range: [0, 1], default: 0.6)
-m           [optional] the sample is male. By default the sample is considered female

Example

./fuwa -i example.bam -o example.output -r reference/ -d dbSNP141.gz -q 0.3 -s 0.3

The BAM file for test can be obtained using the following command:

wget -c http://rubywu.cn/public/example.bam