推荐一个SAM文件中flag含义解释工具

2012/02/04314,739

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><input type="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>

推荐一个SAM文件中flag含义解释工具

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