{"__v":3,"_id":"576bbf60fb62dd20001cda5d","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"576bc92afb62dd20001cda85","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-23T11:34:02.608Z","from_sync":false,"order":21,"slug":"interactive-analysis","title":"INTERACTIVE ANALYSIS"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"566590c83889610d0008a253","version":{"__v":37,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-23T10:52:16.314Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"The Picard Alignment Summary Metrics application is a quality control tool for Exome-Seq and RNA-Seq alignments.\n\nIt compares an alignment file (either BAM or SAM) to the reference file (FASTA), and provides statistics to assess the alignment, such as the number of input reads and the percent of reads that are mapped.\n\nAn Alignment Summary Metrics report is available for all files with the extension .**summary_metrics.txt**.\nClick any file with the extension **.summary_metrics.txt** to access its summary report.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/wpI0ziiuRTWT6a7GjPNI_picard1.jpeg\",\n        \"picard1.jpeg\",\n        \"1597\",\n        \"460\",\n        \"#537b91\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n \nTo see the full list of metrics reported by Alignment Summary Metrics , click **Show details** on its summary report.\n\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/nPs6tmpgTLWxG4s7LpnX_picard2.jpeg\",\n        \"picard2.jpeg\",\n        \"1901\",\n        \"963\",\n        \"#5d93c3\",\n        \"\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\nFor a full explanation of the information shown in the report, we refer you to the <a href=\"https://cgc.sbgenomics.com/public/apps#tool/djordje_klisic/public-apps-by-seven-bridges/picard-collectalignmentsummarymetrics-1-140\" target=\"blank\">package tutorial</a>.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a name=\"top\"></a>","slug":"alignment-summary-metrics","type":"basic","title":"Picard Alignment Summary metrics"}

Picard Alignment Summary metrics

<a name="top"></a>

The Picard Alignment Summary Metrics application is a quality control tool for Exome-Seq and RNA-Seq alignments. It compares an alignment file (either BAM or SAM) to the reference file (FASTA), and provides statistics to assess the alignment, such as the number of input reads and the percent of reads that are mapped. An Alignment Summary Metrics report is available for all files with the extension .**summary_metrics.txt**. Click any file with the extension **.summary_metrics.txt** to access its summary report. [block:image] { "images": [ { "image": [ "https://files.readme.io/wpI0ziiuRTWT6a7GjPNI_picard1.jpeg", "picard1.jpeg", "1597", "460", "#537b91", "" ], "border": true } ] } [/block] To see the full list of metrics reported by Alignment Summary Metrics , click **Show details** on its summary report. [block:image] { "images": [ { "image": [ "https://files.readme.io/nPs6tmpgTLWxG4s7LpnX_picard2.jpeg", "picard2.jpeg", "1901", "963", "#5d93c3", "" ], "border": true } ] } [/block] For a full explanation of the information shown in the report, we refer you to the <a href="https://cgc.sbgenomics.com/public/apps#tool/djordje_klisic/public-apps-by-seven-bridges/picard-collectalignmentsummarymetrics-1-140" target="blank">package tutorial</a>. <div align="right"><a href="#top">top</a></div>