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。
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | <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 += " " + 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: <input id="tb" type="text" size="10"> <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();'> " +lstFlags[i][0] + "</input><br>"); } </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><input type="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> <br> Summary:<br> <div id="summary"> </div></form></body></html> |
