推荐一个SAM文件中flag含义解释工具--转载

SAM是Sequence Alignment/Map 的缩写。像bwa等软件序列比对结果都会输出这样的文件。samtools网站上有专门的文档介绍SAM文件。具体地址：http://samtools.sourceforge.net/SAM1.pdf

很多人困惑SAM文件中的第二列FLAG值是什么意思。根据文档介绍我们可以计算，但是为了方便大家，下面给大家提供一个脚本工具，大家直接输入flag值就可以知道它代表的含义了。

该脚本的使用方法如下截图所示：

脚本工具的使用方法：

将下面的代码保存在记事本里面，另存为一个html文件，如文件名：FlagExplain.html（拓展名一定要为.html）。双击既可以在浏览器里面打开了。

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<html><head><meta http-equiv="Content-Type" content="text/html; charset=GBK">

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   <title>Explain SAM Flags</title>

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   <script type="text/javascript">

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      lstFlags = [["read paired", 0x1],

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             ["read mapped in proper pair", 0x2],

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             ["read unmapped", 0x4],

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             ["mate unmapped", 0x8],

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             ["read reverse strand", 0x10],

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             ["mate reverse strand", 0x20],

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             ["first in pair", 0x40],

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             ["second in pair", 0x80],

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             ["not primary alignment", 0x100],

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             ["read fails platform/vendor quality checks", 0x200],

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             ["read is PCR or optical duplicate", 0x400]];

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      function explainFlags() {

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         var flagValue = parseInt(document.getElementById('tb').value); //returns 0 or NaN if can't parse

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         var summary = "";

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         for(var i = 0; i < lstFlags.length; i++) {

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            var checkbox = document.getElementById('cb' + i)

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            if(lstFlags[i][1] & flagValue) {

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               summary  += " &nbsp; &nbsp; " + lstFlags[i][0] + "<br>";

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               checkbox.checked = true;

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            } else {

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               checkbox.checked = false;

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            }

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         }

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         document.getElementById('summary').innerHTML = summary;

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      }

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      function checkboxClicked() {

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         //compute the new flag value

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         var newFlagValue = 0;

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         for(var i = 0; i < lstFlags.length; i++) {

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            var checkBox = document.getElementById('cb' + i);

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            if(checkBox.checked) {

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               newFlagValue |= lstFlags[i][1];

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            }

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         }

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         var textbox = document.getElementById('tb');

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         textbox.value = newFlagValue;

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         explainFlags();

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      }

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   </script>

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   <noscript>This page requires JavaScript. Please enable it in your browser settings.</noscript>

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</head>

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<body>

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This utility explains SAM flags in plain English. <br>

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<br>

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<form onsubmit="explainFlags(); return false;">

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Flag: &nbsp;

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<input id="tb" type="text" size="10"> &nbsp; &nbsp; &nbsp;

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<input type="submit" value="Explain"><br>

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<br>

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Explanation:<br>

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<script type="text/javascript">

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for(var i = 0; i < lstFlags.length; i++) {

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   document.write("<input type=checkbox name=cb" + i + " id='cb" + i + "'onclick='checkboxClicked();'> &nbsp; " +lstFlags[i][0] + "</input><br>");

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}

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</script><input type="checkbox" name="cb0" id="cb0"onclick="checkboxClicked();"> &nbsp; read paired<br><input type="checkbox"name="cb1" id="cb1" onclick="checkboxClicked();"> &nbsp; read mapped in proper pair<br><input type="checkbox" name="cb2" id="cb2"onclick="checkboxClicked();"> &nbsp; read unmapped<br><input type="checkbox"name="cb3" id="cb3" onclick="checkboxClicked();"> &nbsp; mate unmapped<br><input type="checkbox" name="cb4" id="cb4" onclick="checkboxClicked();"> &nbsp; read reverse strand<br><input type="checkbox" name="cb5" id="cb5"onclick="checkboxClicked();"> &nbsp; mate reverse strand<br><inputtype="checkbox" name="cb6" id="cb6" onclick="checkboxClicked();"> &nbsp; first in pair<br><input type="checkbox" name="cb7" id="cb7"onclick="checkboxClicked();"> &nbsp; second in pair<br><input type="checkbox"name="cb8" id="cb8" onclick="checkboxClicked();"> &nbsp; not primary alignment<br><input type="checkbox" name="cb9" id="cb9"onclick="checkboxClicked();"> &nbsp; read fails platform/vendor quality checks<br><input type="checkbox" name="cb10" id="cb10"onclick="checkboxClicked();"> &nbsp; read is PCR or optical duplicate<br>

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<br>

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Summary:<br>

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<div id="summary">

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</div></form></body></html>