{"id":699,"date":"2026-06-18T15:55:46","date_gmt":"2026-06-18T07:55:46","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=699"},"modified":"2026-06-18T17:41:49","modified_gmt":"2026-06-18T09:41:49","slug":"%e4%bd%bf%e7%94%a8gridss2%e8%bf%9b%e8%a1%8csv%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2026\/06\/18\/%e4%bd%bf%e7%94%a8gridss2%e8%bf%9b%e8%a1%8csv%e5%88%86%e6%9e%90\/","title":{"rendered":"\u4f7f\u7528GRIDSS2\u8fdb\u884cSV\u5206\u6790"},"content":{"rendered":"<p>\u5b98\u65b9github\uff1a<a href=\"https:\/\/github.com\/PapenfussLab\/gridss\/blob\/master\/QuickStart.md\">https:\/\/github.com\/PapenfussLab\/gridss\/blob\/master\/QuickStart.md<\/a><\/p>\n<p>\u53c2\u8003\u6587\u4ef6\u4e0b\u8f7d\uff1a<br \/>\nPON\u6587\u4ef6\uff1a<a href=\"https:\/\/www.bcgsc.ca\/downloads\/morinlab\/hmftools-references\/gridss\/pon\/\">https:\/\/www.bcgsc.ca\/downloads\/morinlab\/hmftools-references\/gridss\/pon\/<\/a> (\u9700\u8981\u628a gridss_pon_breakpoint.hg38.bedpe \u548c gridss_pon_single_breakend.hg38.bed\u6539\u4e3agridss_pon_breakpoint.bedpe\uff0cgridss_pon_single_breakend.bed \u624d\u80fd\u7528)<br \/>\nconda\u5b89\u88c5\u540e\u9700\u989d\u5916\u4e0b\u8f7d\u7684jar\u6587\u4ef6\uff1a<a href=\"https:\/\/github.com\/PapenfussLab\/GRIDSS\/releases\">https:\/\/github.com\/PapenfussLab\/GRIDSS\/releases<\/a><br \/>\nblacklist bed: <a href=\"https:\/\/github.com\/PapenfussLab\/gridss\/tree\/master\/example\">https:\/\/github.com\/PapenfussLab\/gridss\/tree\/master\/example<\/a><\/p>\n<p>\u6279\u91cf\u8fd0\u884c\u811a\u672c\uff1a<\/p>\n<pre><code>perl -ne &#039;chomp; next if \/^$\/; @a = split \/\\t\/; print &quot;gridss -r \/home\/zhoukaiwen\/database\/gridss\/genecode_GRCh38.p14.genome.fa -w $a[0].work -j  \/home\/zhoukaiwen\/software\/gridss-2.13.2-gridss-jar-with-dependencies.jar -o $a[0].somatic.vcf -b \/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed -t 4 ..\/align\/$a[1]_bqsr.bam ..\/align\/$a[0]_bqsr.bam &gt; log\/$a[0].log 2&gt;&amp;1 &amp;&amp; gridss_somatic_filter --pondir \/home\/zhoukaiwen\/database\/gridss\/pondir_hg38\/ --input $a[0].somatic.vcf --output $a[0].high_confidence_somatic.vcf --fulloutput $a[0].high_and_low_confidence_somatic.vcf --scriptdir \\$(dirname\\$(which gridss_somatic_filter)) -n 1 -t 2 &gt;&gt; log\/$a[0].log 2&gt;&amp;1 &amp;&amp; echo $a[0] gridss ok\\n&quot;;&#039; ..\/mutect2\/sample_pair.txt &gt; RunGridss2.sh\n\nnohup bash -c &quot;cat RunGridss2.sh | parallel -j 4&quot; &gt; log\/gridss.log 2&gt;&amp;1 &amp;<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u5b98\u65b9github\uff1ahttps:\/\/github.com\/PapenfussLab\/gridss\/blob\/ma&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-699","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/699","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=699"}],"version-history":[{"count":2,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/699\/revisions"}],"predecessor-version":[{"id":701,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/699\/revisions\/701"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=699"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=699"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=699"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}