{"id":595,"date":"2025-07-03T09:24:45","date_gmt":"2025-07-03T01:24:45","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=595"},"modified":"2025-07-03T10:24:39","modified_gmt":"2025-07-03T02:24:39","slug":"%e4%bd%bf%e7%94%a8fings%e5%af%b9%e7%aa%81%e5%8f%98%e8%bf%9b%e8%a1%8c%e8%bf%87%e6%bb%a4","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2025\/07\/03\/%e4%bd%bf%e7%94%a8fings%e5%af%b9%e7%aa%81%e5%8f%98%e8%bf%9b%e8%a1%8c%e8%bf%87%e6%bb%a4\/","title":{"rendered":"\u4f7f\u7528FiNGS\u5bf9\u7a81\u53d8\u8fdb\u884c\u8fc7\u6ee4"},"content":{"rendered":"<p>\u539f\u6587\uff1a<a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-03995-y\">https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-03995-y<\/a><br \/>\ngithub\uff1a<a href=\"https:\/\/github.com\/cpwardell\/FiNGS\">https:\/\/github.com\/cpwardell\/FiNGS<\/a><\/p>\n<h4>\u5b89\u88c5<\/h4>\n<pre><code>conda create -n fings python=3.7\nconda activate fings\nconda install fings\n\n# Locate the FiNGS package, navigate to the example data and run the script to confirm your installation is correct.\n## Navigate to this directory \/path\/to\/conda\/envs\/fings\/lib\/python3.7\/site-packages\/fings\/exampledata\/\n.\/test.sh\n<\/code><\/pre>\n<h4>\u8fd0\u884c<\/h4>\n<pre><code># \u6784\u5efa\u6279\u91cf\u8fd0\u884c\u811a\u672c\nperl -ne &#039;chomp; next if \/^$\/; @a = split \/\\t\/; print &quot;fings -t ..\/align\/$a[0]_bqsr.bam -n ..\/align\/$a[1]_bqsr.bam -v $a[0].somatic.passed.vcf --PASSonlyin --PASSonlyout -d $a[0]_FiNGS -j 4 &amp;&amp; echo $a[0] FiNGS ok\\n&quot;&#039; sample_pair.txt &gt; RunFiNGS.sh<\/code><\/pre>\n<h4>\u7a81\u53d8\u6ce8\u91ca<\/h4>\n<pre><code>perl -ne &#039;chomp;next if($_=~\/^$\/);my @a=split \/\\t\/;print &quot;vcf2maf.pl --input-vcf $a[0].somatic.passed.filtered.vcf --output-maf $a[0].FiNGS.maf --normal-id $a[1] --tumor-id $a[0] --vcf-tumor-id $a[0] --vcf-normal-id $a[1] --vep-path \/home\/zhoukaiwen\/software\/anaconda3\/envs\/vcf2maf\/bin --vep-data \/home\/zhoukaiwen\/database\/vep\/ --ref-fasta \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa --verbose --ncbi-build GRCh38 --cache-version 114 &amp;&amp; echo $a[0] vcf2maf ok\\n&quot;&#039; ..\/sample_pair.txt &gt;vcf2maf.sh<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u539f\u6587\uff1ahttps:\/\/bmcbioinformatics.biomedcentral.com\/articles&#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-595","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\/595","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=595"}],"version-history":[{"count":3,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/595\/revisions"}],"predecessor-version":[{"id":598,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/595\/revisions\/598"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=595"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=595"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=595"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}