{"id":958,"date":"2019-07-26T21:25:18","date_gmt":"2019-07-26T12:25:18","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=958"},"modified":"2019-10-17T22:16:50","modified_gmt":"2019-10-17T13:16:50","slug":"bioinfovcf%e3%83%95%e3%82%a1%e3%82%a4%e3%83%ab%e3%82%92%e6%af%94%e8%bc%83%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=958","title":{"rendered":"[bioinfo]vcf\u30d5\u30a1\u30a4\u30eb\u3092\u6bd4\u8f03\u3059\u308b"},"content":{"rendered":"<p>bcftool\u3092\u4f7f\u3063\u3066vcf\u30d5\u30a1\u30a4\u30eb\u3092\u6bd4\u8f03\u3059\u308b\u3002<\/p>\n<p>bcftools\u3092\u4f7f\u3046\u305f\u3081\u306b\u306fbgzip\u306b\u3066\u30d5\u30a1\u30a4\u30eb\u3092\u5727\u7e2e\u3057\u3001\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u4ed8\u3051\u308b\u5fc5\u8981\u304c\u3042\u308b\u306e\u3067\u3001\u307e\u305a\u305d\u308c\u3089\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u6e96\u5099\u3059\u308b\u3002<\/p>\n<pre class=\"\">bgzip -threads 8 file_A.vcf\nbgzip -threads 8 file_B.vcf\nbgzip -threads 8 file_C.vcf\n<\/pre>\n\n\n<pre class=\"\">bcftools index file_A.vcf.gz\nbcftools index file_B.vcf.gz\nbcftools index file_C.vcf.gz<\/pre>\n\n\n\n<p>\u4f7f\u3044\u65b9\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\"> bcftools isec [<em>OPTIONS<\/em>] A.vcf.gz B.vcf.gz [..]<\/pre>\n\n\n\n<p>[<em>OPTIONS<\/em>]<\/p>\n\n\n\n<p>-c, &#8211;collapse snps|indels|both|all|some|none<br>     \u6307\u5b9a\u3057\u305f\u7a2e\u985e\u306e\u5909\u7570\u3060\u3051\u51fa\u529b\u3059\u308b<br> -C, &#8211;complement<br>     \u6700\u521d\u306b\u5165\u529b\u3057\u305fvcf\u30d5\u30a1\u30a4\u30eb\u306b\u306e\u307f\u5b58\u5728\u3059\u308b\u5909\u7570\u3092\u51fa\u529b<br> -e, &#8211;exclude -|EXPRESSION<br>     \u5909\u7570\u306e\u7a2e\u985e\u3092\u7d30\u304b\u304f\u8abf\u7bc0\u3059\u308b\u3002\u4f8b\u3048\u3070\u3001\u30b3\u30fc\u30eb\u30af\u30aa\u30ea\u30c6\u30a350\u4ee5\u4e0b\u3092\u6392\u9664\u3059\u308b\u306a\u3089\u3001<br>-e AVG(GQ)>50<br> -f, &#8211;apply-filters LIST<br>     \u5225\u30d5\u30a1\u30a4\u30eb\u3067\u7528\u610f\u3057\u305ffilter\u30ea\u30b9\u30c8\u3092\u9069\u7528\u3059\u308b<br> -i, &#8211;include EXPRESSION<br>    -e\u306e\u9006\u3001true\u3068\u306a\u308b\u6761\u4ef6\u3092\u6b8b\u3059\u3002<br> -n, &#8211;nfiles [+-=]INT|~BITMAP<br>     output positions present in this many (=), this many or more (+), this many or fewer (-), or the exact same (~) files <br> -o, &#8211;output FILE<br>     see Common Options. When several files are being output, their names are controlled via -p instead. <br> -O, &#8211;output-type b|u|z|v<br>     see Common Options <br> -p, &#8211;prefix DIR<br>     \u51fa\u529b\u3059\u308b\u30d5\u30a9\u30eb\u30c0\u3092\u6307\u5b9a\u3002<br> -r, &#8211;regions chr|chr:pos|chr:from-to|chr:from-[,\u2026]<br>     see Common Options <br> -R, &#8211;regions-file file<br>     see Common Options <br> -t, &#8211;targets chr|chr:pos|chr:from-to|chr:from-[,\u2026]<br>     see Common Options <br> -T, &#8211;targets-file file<br>     see Common Options <br> -w, &#8211;write LIST<br>     list of input files to output given as 1-based indices. With -p and no -w, all files are written. <\/p>\n\n\n","protected":false},"excerpt":{"rendered":"<p>bcftool\u3092\u4f7f\u3063\u3066vcf\u30d5\u30a1\u30a4\u30eb\u3092\u6bd4<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","_locale":"ja","_original_post":"958","footnotes":""},"categories":[7],"tags":[],"class_list":["post-958","post","type-post","status-publish","format-standard","hentry","category-protocol","ja"],"_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/958","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=958"}],"version-history":[{"count":5,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/958\/revisions"}],"predecessor-version":[{"id":1072,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/958\/revisions\/1072"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=958"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=958"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=958"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}