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推荐一个SAM文件中flag含义解释工具--转载

2017-02-03 16:57 639 查看
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
varflagValue =parseInt(document.getElementById('tb').value); //returns 0 or NaN if can't parse
18
varsummary ="";
19
for(vari =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
varnewFlagValue =0;
35
for(vari =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(vari =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
><
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
>
65
<
br
>
66
Summary:<
br
>
67
<
div
 
id
=
"summary"
>
68
</
div
></
form
></
body
></
html
>

                                            

                                        

                        
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