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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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 += " " + lstFlags[i][0] + "<br>"; |
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checkbox.checked = true; |
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checkbox.checked = false; |
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document.getElementById('summary').innerHTML = summary; |
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function checkboxClicked() { |
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//compute the new flag value |
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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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var textbox = document.getElementById('tb'); |
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textbox.value = newFlagValue; |
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<noscript>This page requires JavaScript. Please enable it in your browser settings.</noscript> |
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This utility explains SAM flags in plain English. <br> |
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<form onsubmit="explainFlags(); return false;"> |
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<input id="tb" type="text" size="10"> |
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<input type="submit" value="Explain"><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();'> " +lstFlags[i][0] + "</input><br>"); |
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</script><input type="checkbox" name="cb0" id="cb0" onclick="checkboxClicked();"> read paired<br><input type="checkbox" name="cb1" id="cb1"onclick="checkboxClicked();"> read mapped in proper pair<br><inputtype="checkbox" name="cb2" id="cb2" onclick="checkboxClicked();"> read unmapped<br><input type="checkbox" name="cb3" id="cb3" onclick="checkboxClicked();"> mate unmapped<br><input type="checkbox" name="cb4" id="cb4" onclick="checkboxClicked();"> read reverse strand<br><input type="checkbox" name="cb5" id="cb5" onclick="checkboxClicked();"> mate reverse strand<br><input type="checkbox" name="cb6" id="cb6" onclick="checkboxClicked();"> first in pair<br><input type="checkbox" name="cb7" id="cb7" onclick="checkboxClicked();"> second in pair<br><input type="checkbox" name="cb8" id="cb8"onclick="checkboxClicked();"> not primary alignment<br><input type="checkbox" name="cb9" id="cb9" onclick="checkboxClicked();"> read fails platform/vendor quality checks<br><input type="checkbox" name="cb10" id="cb10" onclick="checkboxClicked();"> read is PCR or optical duplicate<br> |
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</div></form></body></html> |
参考：https://www.plob.org/article/1697.html