Fig. 1
From: A study on fast calling variants from next-generation sequencing data using decision tree
Workflow of Fuwa. Fuwa is designed to translate single BAM file into high quality variants calling output in VCF format. At first, aligner such as BWA maps reads to reference genome and provides BAM file to Fuwa. Then, at each locus of genome, candidate variants are generated from the CIGAR field of piled up reads covering that locus. Each candidate variant is assigned a 0/1 value named dbSNP quality (qual), according to whether it is included in dbSNP. Next, the candidate set is used to build a decision tree. After the tree is build, qual values of variants in the same leaf will be replaced with the average qual value of that leaf. Finally, Candidate variants with low qual (default threshold 0.8) are filtered out, while the rest are called and genotyped. Final call set is output in VCF format