Overview
HapMonster is a Java program that enables simultaneous variant calling and haplotype phasing for next generation sequencing data. Phased haplotypes are estimated based on phase-informative reads which span multiple heterozygous variant sites.
Input
The sequence read data in SAM or BAM format (BAM file with BAQ information is recommended)
Output
Variant calling and haplotype phasing results in VCF format
Usage
Example
java -jar HapMonster.jar \
VariantCall \
-r reference_genome.fasta \
-t chr1 \
-d average_depth \
-il true \
<SAM or BAM file> \
<VCF file>
Options
| Option | Default Value | Summary |
-r (--reference) STR |
none | Reference genome fasta file* |
-d (--depth) INT |
none | Read coverage* |
-t (--target-region) STR |
none | Target region for variant calling* |
-c (--call-range-size) INT |
2500000 | Variant calling range size |
-h (--help) |
false | Print options and exit |
-i (--iteration) INT |
20 | Iteration count |
-il (--illumina) [true/false] |
false | Use Illumina HiSeq read correction mode |
-l (--depth-limit) INT |
500 | Depth limit |
-m (--margin) INT |
1000 | Margin for variant calling |
-p (--use-paired-end) [true/false] |
true | Consider paired-end reads |
-rp (--reference-prior) DOUBLE |
0.135 | Prior strength for reference allele |
-th (--threshold) DOUBLE |
10.0 | Threshold for filtering variant calls |
-u (--unit-id) INT |
1 | Unit ID |
* Required options
Download
- Jar file only: HapMonster.jar
- Jar file and example data: HapMonster.tgz
Citation
Please cite the following manuscript related to this software:
Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata,
Yukuto Sato, Yosuke Kawai and Masao Nagasaki,
HapMonster: a Statistically Unified Approach for Variant Calling and
Haplotyping Based on Phase-informative Reads,
Lecture Notes in Bioinformatics, 8542, 107-118 (2014) (3/Jul/2014)
https://link.springer.com/chapter/10.1007/978-3-319-07953-0_9