推荐一个SAM文件或者bam文件中flag含义解释工具

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。

查看源代码

打印帮助

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

`02`	`<title>Explain SAM Flags</title>`

`03`	`<script` `type="text/javascript">`

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

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

`06`	`["read unmapped", 0x4],`

`07`	`["mate unmapped", 0x8],`

`08`	`["read reverse strand", 0x10],`

`09`	`["mate reverse strand", 0x20],`

`10`	`["first in pair", 0x40],`

`11`	`["second in pair", 0x80],`

`12`	`["not primary alignment", 0x100],`

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

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

15

`16`	`function explainFlags() {`

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

`18`	`var summary = "";`

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

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

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

`22`	`summary += "     " + lstFlags[i][0] + "<br>";`

`23`	`checkbox.checked = true;`

`24`	`} else {`

`25`	`checkbox.checked = false;`

26 }

27 }

28

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

30 }

31

`32`	`function checkboxClicked() {`

`33`	`//compute the new flag value`

`34`	`var newFlagValue = 0;`

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

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

`37`	`if(checkBox.checked) {`

`38`	`newFlagValue \|= lstFlags[i][1];`

39 }

40 }

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

`42`	`textbox.value` `=` `newFlagValue;`

`43`	`explainFlags();`

44 }

`45`	`</script>`

46

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

48 </head>

49 <body>

50

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

52 <br>

53

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

55 Flag: 

`56`	`<input` `id="tb"` `type="text"` `size="10">      `

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

58 <br>

`59`	`Explanation:<br>`

`60`	`<script` `type="text/javascript">`

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

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

63 }

64 </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>

65 <br>

`66`	`Summary:<br>`

`67`	`<div` `id="summary">`

`68`	`</div></form></body></html>`

参考：https://www.plob.org/article/1697.html