HapMonster

hapmonster

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

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