{"id":1566,"date":"2014-01-07T17:41:05","date_gmt":"2014-01-07T08:41:05","guid":{"rendered":"http:\/\/nagasakilab.csml.org\/ja\/?page_id=1566"},"modified":"2017-08-21T16:04:53","modified_gmt":"2017-08-21T07:04:53","slug":"hapmonster","status":"publish","type":"page","link":"https:\/\/nagasakilab.csml.org\/ja\/hapmonster","title":{"rendered":"HapMonster"},"content":{"rendered":"<h3 class=\"sub\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2375\" src=\"http:\/\/nagasakilab.csml.org\/ja\/wp-content\/uploads\/2014\/01\/hapmonster.png\" alt=\"hapmonster\" width=\"300\" height=\"178\"><br \/>\n\u6982\u8981<\/h3>\n<p style=\"padding-left: 30px;\">HapMonster \u306f\u3001NGS \u30c7\u30fc\u30bf\u304b\u3089\u5909\u7570\u30b3\u30fc\u30eb\u3068\u30cf\u30d7\u30ed\u30bf\u30a4\u30d7\u30d5\u30a7\u30fc\u30b8\u30f3\u30b0\u3092\u540c\u6642\u306b\u884c\u3046 Java \u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u3059\u3002\u8907\u6570\u306e\u30d8\u30c6\u30ed\u63a5\u5408\u30b5\u30a4\u30c8\u306b\u307e\u305f\u3050 phase-informative read \u3092\u7528\u3044\u3066\u30d5\u30a7\u30fc\u30b8\u30f3\u30b0\u3092\u884c\u3044\u307e\u3059\u3002<\/p>\n<h3 class=\"sub\">\u5165\u529b\u30d5\u30a1\u30a4\u30eb<\/h3>\n<p style=\"padding-left: 30px;\">SAM \u307e\u305f\u306f BAM \u30d5\u30a9\u30fc\u30de\u30c3\u30c8\u3067\u4fdd\u5b58\u3055\u308c\u305f NGS \u30c7\u30fc\u30bf\uff08BAQ \u60c5\u5831\u304c\u4ed8\u52a0\u3055\u308c\u305f BAM \u30d5\u30a1\u30a4\u30eb\u63a8\u5968\uff09<\/p>\n<h3 class=\"sub\">\u51fa\u529b\u30d5\u30a1\u30a4\u30eb<\/h3>\n<p style=\"padding-left: 30px;\">\u5909\u7570\u30b3\u30fc\u30eb\u3068\u30d5\u30a7\u30fc\u30b8\u30f3\u30b0\u7d50\u679c\u3092 VCF \u30d5\u30a9\u30fc\u30de\u30c3\u30c8\u3067\u51fa\u529b<\/p>\n<h3 class=\"sub\">\u4f7f\u7528\u65b9\u6cd5<\/h3>\n<p style=\"padding-left: 30px;\">\u4f7f\u7528\u4f8b<\/p>\n<blockquote>\n<pre>  java -jar HapMonster.jar \\\r\n    VariantCall \\\r\n    -r reference_genome.fasta \\\r\n    -t chr1 \\\r\n    -d average_depth \\\r\n    -il true \\\r\n    &lt;SAM or BAM file&gt; \\\r\n    &lt;VCF file&gt;<\/pre>\n<\/blockquote>\n<h3 class=\"sub\">\u30aa\u30d7\u30b7\u30e7\u30f3<\/h3>\n<table style=\"margin-left: 30px; margin-top: 30px;\" border=\"1\" cellspacing=\"0\" cellpadding=\"0\">\n<tbody>\n<tr>\n<td valign=\"top\" width=\"142\"><b>\u30aa\u30d7\u30b7\u30e7\u30f3<\/b><\/td>\n<td valign=\"top\" width=\"142\"><b>\u30c7\u30d5\u30a9\u30eb\u30c8\u5024<\/b><\/td>\n<td valign=\"top\" width=\"142\"><b>\u5185\u5bb9<\/b><\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-r (--reference) STR<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">&#8211;<\/td>\n<td valign=\"top\" width=\"142\">\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u30b2\u30ce\u30e0\u7528 fasta \u30d5\u30a1\u30a4\u30eb*<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-d (--depth) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">&#8211;<\/td>\n<td valign=\"top\" width=\"142\">\u30c7\u30fc\u30bf\u306e\u5e73\u5747\u6df1\u5ea6*<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-t (--target-region) STR<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">&#8211;<\/td>\n<td valign=\"top\" width=\"142\">\u5909\u7570\u30b3\u30fc\u30eb\u5bfe\u8c61\u9818\u57df*<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-c (--call-range-size) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">2500000<\/td>\n<td valign=\"top\" width=\"142\">\u5909\u7570\u30b3\u30fc\u30eb\u30ec\u30f3\u30b8\u30b5\u30a4\u30ba<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-h (--help)<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">&#8211;<\/td>\n<td valign=\"top\" width=\"142\">\u30aa\u30d7\u30b7\u30e7\u30f3\u60c5\u5831<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-i (--iteration) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">20<\/td>\n<td valign=\"top\" width=\"142\">\u53cd\u5fa9\u56de\u6570<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-il (--illumina) [true\/false]<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">false<\/td>\n<td valign=\"top\" width=\"142\">Illumina HiSeq \u30c7\u30fc\u30bf\u7279\u6027\u306e\u4fee\u6b63<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-l (--depth-limit) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">500<\/td>\n<td valign=\"top\" width=\"142\">\u6df1\u5ea6\u306e\u30ea\u30df\u30c3\u30c8<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-m (--margin) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">1000<\/td>\n<td valign=\"top\" width=\"142\">\u5909\u7570\u30b3\u30fc\u30eb\u9593\u306e\u30de\u30fc\u30b8\u30f3\u30b5\u30a4\u30ba<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-p (--use-paired-end) [true\/false]<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">true<\/td>\n<td valign=\"top\" width=\"142\">\u30da\u30a2\u30c9\u30a8\u30f3\u30c9\u3092\u8003\u616e<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-rp (--reference-prior) DOUBLE<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">0.135<\/td>\n<td valign=\"top\" width=\"142\">\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u30a2\u30ea\u30eb\u5f37\u5ea6<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-th (--threshold) DOUBLE<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">10.0<\/td>\n<td valign=\"top\" width=\"142\">\u5909\u7570\u30b3\u30fc\u30eb\u30d5\u30a3\u30eb\u30bf\u30ea\u30f3\u30b0\u95be\u5024<\/td>\n<\/tr>\n<tr>\n<td valign=\"top\" width=\"142\">\n<pre>-u (--unit-id) INT<\/pre>\n<\/td>\n<td valign=\"top\" width=\"142\">1<\/td>\n<td valign=\"top\" width=\"142\">\u30e6\u30cb\u30c3\u30c8 ID<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>* \u5fc5\u9808\u30aa\u30d7\u30b7\u30e7\u30f3<\/p>\n<h3 class=\"sub\">\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/h3>\n<ul>\n<li>Jar \u30d5\u30a1\u30a4\u30eb\u306e\u307f\uff1a&nbsp;<a href=\"http:\/\/nagasakilab.csml.org\/data\/HapMonster.jar\">HapMonster.jar<\/a><\/li>\n<li>Jar \u30d5\u30a1\u30a4\u30eb\u3068 example \u30c7\u30fc\u30bf\uff1a&nbsp;<a href=\"http:\/\/nagasakilab.csml.org\/data\/HapMonster.tgz\">HapMonster.tgz<\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><strong>\u203b\u5f15\u7528\u306b\u3064\u3044\u3066<\/strong><br \/>\n<strong> \u3053\u306e\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306b\u95a2\u9023\u3057\u305f\u5f15\u7528\u306f\u4ee5\u4e0b\u306e\u8ad6\u6587\u306b\u306a\u308a\u307e\u3059\u3002<\/strong><\/p>\n<hr>\n<p>Kaname Kojima, Naoki Nariai, Takahiro Mimori, Yumi Yamaguchi-Kabata,<br \/>\nYukuto Sato, Yosuke Kawai and Masao Nagasaki,<br \/>\nHapMonster: a Statistically Unified Approach for Variant Calling and<br \/>\nHaplotyping Based on Phase-informative Reads,<br \/>\nLecture Notes in Bioinformatics, 8542, 107-118 (2014) (3\/Jul\/2014)<\/p>\n<p><a href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-07953-0_9\">https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-07953-0_9<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u6982\u8981 HapMonster \u306f\u3001NGS \u30c7\u30fc\u30bf\u304b\u3089\u5909\u7570\u30b3\u30fc\u30eb\u3068\u30cf\u30d7\u30ed\u30bf\u30a4\u30d7\u30d5\u30a7\u30fc &hellip; <a href=\"https:\/\/nagasakilab.csml.org\/ja\/hapmonster\">\u7d9a\u304d\u3092\u8aad\u3080 <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1566","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/pages\/1566","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/comments?post=1566"}],"version-history":[{"count":32,"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/pages\/1566\/revisions"}],"predecessor-version":[{"id":2377,"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/pages\/1566\/revisions\/2377"}],"wp:attachment":[{"href":"https:\/\/nagasakilab.csml.org\/ja\/wp-json\/wp\/v2\/media?parent=1566"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}