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：

推荐一个SAM文件中flag含义解释工具

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
 
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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  += " &nbsp; &nbsp; " + 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: &nbsp;
56 <input id="tb" type="text" size="10"> &nbsp; &nbsp; &nbsp;
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();'> &nbsp; " +lstFlags[i][0] + "</input><br>");
63 }
64 </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>
65 <br>
66 Summary:<br>
67 <div id="summary">
68 </div></form></body></html>
posted @ 2017-02-03 16:57  nkwy2012  阅读(2114)  评论(0)    收藏  举报