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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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Author: Mengyao Zhao
Contact: Mengyao Zhao <zhangmp@bc.edu>
Last revision: 02/11/2014

1. 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).

2. 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.

3. Run PHV
Usage:   region [options] <reference.fasta> <alignment.bam> [region1 [...]]

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.

4. Output of PHV
The output of PHV is the genomic variation in VCF format. Please see the description of VCF format at http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41.