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。
Explain SAM FlagslstFlags = [["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] + "
";
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();
}
This page requires JavaScript. Please enable it in your browser settings.This utility explains SAM flags in plain English.
Flag:
Explanation:
for(var i = 0; i < lstFlags.length; i++) {
document.write(" " +lstFlags[i][0] + "
");
}
read paired read mapped in proper pair read unmapped mate unmapped read reverse strand mate reverse strand first in pair second in pair not primary alignment read fails platform/vendor quality checks read is PCR or optical duplicate
Summary:
