PHV: an accurate SNP and INDEL caller based on the Profile Hidden Markov Model
License: MIT
Copyright (c) 2012-2015 Boston College
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Author: Mengyao Zhao Contact: Mengyao Zhao zhangmp@bc.edu Last revision: 02/11/2014
Overview PHV is an accurate SNP and INDEL caller based on the Profile Hidden Markov Model. Different from most other variant callers, PHV does not rely on the single alignment generated by the aligners. Instead, it considers all possible alignments of the reads together by learning from the given data. Therefore, PHV can give more accurate variant calls. On our testing data set, PHV’s SNP detection is already better than GATK and Samtools. PHV takes reference file (in FASTA format) and alignemnt file (in BAM format) as inputs, and outputs the genomic variations (in VCF format).
Install PHV 1) Download the software from https://github.com/mengyao/PHMM-SNP-INDEL-caller. 2) cd src 3) make 4) The executable file will be region.
Run PHV
Usage: region [options]
Options: -s N N is the largest detectable INDEL length. [default: 100] Notes:
A region should be presented in one of the following formats:
`chr1', `chr2:1,000' and `chr3:1,000-2,000'. When a region is
specified, the input alignment file must be an indexed BAM file.