{"id":774,"date":"2014-02-17T19:49:23","date_gmt":"2014-02-17T10:49:23","guid":{"rendered":"http:\/\/nagasakilab.csml.org\/en\/?page_id=774"},"modified":"2024-02-16T09:34:01","modified_gmt":"2024-02-16T00:34:01","slug":"hapmonster","status":"publish","type":"page","link":"https:\/\/nagasakilab.csml.org\/en\/hapmonster","title":{"rendered":"HapMonster"},"content":{"rendered":"

\"hapmonster\"<\/h3>\n

Overview
\n<\/strong><\/h3>\n

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.<\/p>\n

Input
\n<\/strong><\/h3>\n

The sequence read data in SAM or BAM format (BAM file with BAQ information is recommended)<\/p>\n

Output<\/strong><\/h3>\n

Variant calling and haplotype phasing results in VCF format<\/p>\n

Usage<\/strong><\/h3>\n

Example<\/p>\n

\n
  java -jar HapMonster.jar \\\n    VariantCall \\\n    -r reference_genome.fasta \\\n    -t chr1 \\\n    -d average_depth \\\n    -il true \\\n    <SAM or BAM file> \\\n    <VCF file><\/pre>\n<\/blockquote>\n
Options<\/strong><\/h3>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Option<\/b><\/td>\nDefault Value<\/b><\/td>\nSummary<\/b><\/td>\n<\/tr>\n
\n
-r (--reference) STR<\/pre>\n<\/td>\n
none<\/td>\nReference genome fasta file*<\/td>\n<\/tr>\n
\n
-d (--depth) INT<\/pre>\n<\/td>\n
none<\/td>\nRead coverage*<\/td>\n<\/tr>\n
\n
-t (--target-region) STR<\/pre>\n<\/td>\n
none<\/td>\nTarget region for variant calling*<\/td>\n<\/tr>\n
\n
-c (--call-range-size) INT<\/pre>\n<\/td>\n
2500000<\/td>\nVariant calling range size<\/td>\n<\/tr>\n
\n
-h (--help)<\/pre>\n<\/td>\n
false<\/td>\nPrint options and exit<\/td>\n<\/tr>\n
\n
-i (--iteration) INT<\/pre>\n<\/td>\n
20<\/td>\nIteration count<\/td>\n<\/tr>\n
\n
-il (--illumina) [true\/false]<\/pre>\n<\/td>\n
false<\/td>\nUse Illumina HiSeq read correction mode<\/td>\n<\/tr>\n
\n
-l (--depth-limit) INT<\/pre>\n<\/td>\n
500<\/td>\nDepth limit<\/td>\n<\/tr>\n
\n
-m (--margin) INT<\/pre>\n<\/td>\n
1000<\/td>\nMargin for variant calling<\/td>\n<\/tr>\n
\n
-p (--use-paired-end) [true\/false]<\/pre>\n<\/td>\n
true<\/td>\nConsider paired-end reads<\/td>\n<\/tr>\n
\n
-rp (--reference-prior) DOUBLE<\/pre>\n<\/td>\n
0.135<\/td>\nPrior strength for reference allele<\/td>\n<\/tr>\n
\n
-th (--threshold) DOUBLE<\/pre>\n<\/td>\n
10.0<\/td>\nThreshold for filtering variant calls<\/td>\n<\/tr>\n
\n
-u (--unit-id) INT<\/pre>\n<\/td>\n
1<\/td>\nUnit ID<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
* Required options<\/p>\n
Download<\/strong><\/h3>\n