A decision-tree-based fast variant caller.
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.
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
./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