{"id":2820,"date":"2024-12-17T21:08:38","date_gmt":"2024-12-17T12:08:38","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2820"},"modified":"2024-12-17T21:20:40","modified_gmt":"2024-12-17T12:20:40","slug":"bioinfostar%e3%81%a7mapping%e3%81%97%e3%81%9f%e3%83%87%e3%83%bc%e3%82%bf%e3%82%92gatk%e3%81%a7snp-call%e3%81%99%e3%82%8b%e9%9a%9b%e3%81%aetips","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2820","title":{"rendered":"[bioinfo]STAR\u3067mapping\u3057\u305f\u30c7\u30fc\u30bf\u3092gatk\u3067snp call\u3059\u308b\u969b\u306etips"},"content":{"rendered":"\n<p>STAR\u3067mapping\u3057\u3066bam\u51fa\u529b\u3057\u305f\u3082\u306e\u3092gatk\u3067MarkDuplicates\u3057\u3088\u3046\u3068\u3059\u308b\u3068\u3001<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>&#91;Tue Dec 17 20:53:31 JST 2024] Executing as igawa@igawa-XXXX on Linux 5.19.0-32-generic amd64; OpenJDK 64-Bit Server VM 22.0.1-internal-adhoc.conda.src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.6.1.0\nINFO\t2024-12-17 20:53:31\tMarkDuplicates\tStart of doWork freeMemory: 88456088; totalMemory: 117440512; maxMemory: 16642998272\nINFO\t2024-12-17 20:53:31\tMarkDuplicates\tReading input file and constructing read end information.\nINFO\t2024-12-17 20:53:31\tMarkDuplicates\tWill retain up to 60300718 data points before spilling to disk.\n&#91;Tue Dec 17 20:53:31 JST 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.\nRuntime.totalMemory()=897581056\nTo get help, see http:\/\/broadinstitute.github.io\/picard\/index.html#GettingHelp\njava.lang.NullPointerException: Cannot invoke \"htsjdk.samtools.SAMReadGroupRecord.getReadGroupId()\" because the return value of \"htsjdk.samtools.SAMRecord.getReadGroup()\" is null\n\tat picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:558)\n\tat picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:270)\n\tat picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)\n\tat org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)\n\tat org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)\n\tat org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)\n\tat org.broadinstitute.hellbender.Main.main(Main.java:306)<\/code><\/pre>\n\n\n\n<p>\u306a\u3069\u3068\u8868\u793a\u3055\u308c\u3001\u4e00\u898b\u5b9f\u884c\u3057\u305f\u3088\u3046\u306b\u898b\u3048\u3066\u3001\u30a8\u30e9\u30fc\u7d42\u4e86\u3068\u306a\u308b\u3002\u3053\u308c\u306f\u3001STAR\u304c\u51fa\u529b\u3059\u308bbam\u306e\u30d8\u30c3\u30c0\u30fc\u306breadgroup (=@RG)\u304c\u306a\u3044\u3053\u3068\u304c\u539f\u56e0\u3089\u3057\u304f\u3001<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>samtools addreplacerg -r \"@RG\\tID:RG1\\tSM:SampleName\\tPL:Illumina\\tLB:Library.fa\" -o .&lt;output.bam&gt; &lt;input.bam&gt;<\/code><\/pre>\n\n\n\n<p>\u3092\u5b9f\u884c\u3059\u308b\u3068\u89e3\u6c7a\u3059\u308b\u3002<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>STAR\u3067mapping\u3057\u3066bam\u51fa\u529b\u3057<\/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":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2820","footnotes":""},"categories":[7],"tags":[],"class_list":["post-2820","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\/2820","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=2820"}],"version-history":[{"count":7,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2820\/revisions"}],"predecessor-version":[{"id":2827,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2820\/revisions\/2827"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2820"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2820"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2820"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}