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  • 31、SAM文件中flag含义解释工具--转载

    转载:http://www.cnblogs.com/nkwy2012/p/6362996.html

     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。

     

    <html><head><meta http-equiv="Content-Type" content="text/html; charset=GBK">
    <title>Explain SAM Flags</title>
    <script type="text/javascript">
    lstFlags = [["read paired", 0x1],
    ["read mapped in proper pair", 0x2],
    ["read unmapped", 0x4],
    ["mate unmapped", 0x8],
    ["read reverse strand", 0x10],
    ["mate reverse strand", 0x20],
    ["first in pair", 0x40],
    ["second in pair", 0x80],
    ["not primary alignment", 0x100],
    ["read fails platform/vendor quality checks", 0x200],
    ["read is PCR or optical duplicate", 0x400]];

    function explainFlags() {
    var flagValue = parseInt(document.getElementById('tb').value); //returns 0 or NaN if can't parse
    var summary = "";
    for(var i = 0; i < lstFlags.length; i++) {
    var checkbox = document.getElementById('cb' + i)
    if(lstFlags[i][1] & flagValue) {
    summary += " &nbsp; &nbsp; " + lstFlags[i][0] + "<br>";
    checkbox.checked = true;
    } else {
    checkbox.checked = false;
    }
    }

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

    function checkboxClicked() {
    //compute the new flag value
    var newFlagValue = 0;
    for(var i = 0; i < lstFlags.length; i++) {
    var checkBox = document.getElementById('cb' + i);
    if(checkBox.checked) {
    newFlagValue |= lstFlags[i][1];
    }
    }
    var textbox = document.getElementById('tb');
    textbox.value = newFlagValue;
    explainFlags();
    }
    </script>

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

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

    <form onsubmit="explainFlags(); return false;">
    Flag: &nbsp;
    <input id="tb" type="text" size="10"> &nbsp; &nbsp; &nbsp;
    <input type="submit" value="Explain"><br>
    <br>
    Explanation:<br>
    <script type="text/javascript">
    for(var i = 0; i < lstFlags.length; i++) {
    document.write("<input type=checkbox name=cb" + i + " id='cb" + i + "'onclick='checkboxClicked();'> &nbsp; " +lstFlags[i][0] + "</input><br>");
    }
    </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>
    <br>
    Summary:<br>
    <div id="summary">
    </div></form></body></html>

     
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  • 原文地址:https://www.cnblogs.com/renping/p/7435723.html
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