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het. and hom. SNP？
HI,I use MAQ software mapping the reads.
Is there anybody know how to get the het and hom SNPs from MAQ software?
Thx!
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HI,
I use MAQ software mapping the reads.
Is there anybody know how to get the het and hom SNPs from MAQ software?
Thx! -
Hi,
Running the command 'maq cns2snp in.cns > out.snp' should give you the info you are looking for - see http://maq.sourceforge.net/maq-manpage.shtml for output column descriptions.
Q -
Thx Q...
I already Runing the command 'maq cns2snp in.cns > out.snp'.
Now I write a simple perl script to split the snp file to hom snp and het snp.Comment
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No ... no ... no perl ... a one-liner bash with awk will do. Let me know if you need the one-liner ... :-)
QComment
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Really?
I am sorry,I am not familiar with Linux command.
But I'd like to know!
Thanks a million!Comment
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cat MAQ_SNP_FILE | awk '{ if (($4!="A") && ($4!="C") && ($4!="G") && ($4!="T") ) { print $0 } }' > het.snps
cat MAQ_SNP_FILE | awk '{ if (($4=="A") || ($4=="C") || ($4=="G") || ($4=="T") ) { print $0 } }' > homo.snps
$4 means column number 4 in your MAQ_SNP_FILE.
QComment
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Ha~cool!
It's works...
It's better than perl!
faster and just a liner~
Thanks a million!
Thank you Q...Comment
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Perl is also good
Of course perl can be a one-liner as well. And, IMHO, a cleaner one than awk.
perl -nle '@z = split /\t/; print if $z[3] !~ /[ACGT]/' MAQ_SNP_FILE > het.snps
perl -nle '@z = split /\t/; print if $z[3] =~ /[ACGT]/' MAQ_SNP_FILE > homo.snps
Basically, the 'perl -nle' means:
'n' ==> loop through the file
'l' ==> remove and add newlines as needed
'e' ==> execute the following script.
The script is in two parts:
@z = split /\t/ ==> takes the line and splits it along tabs into an array called '@z'
print if the 4th element of the array (called [3] in the perl 0-based array structure) is not (hets) or is (homo) one of A, C, G, or T.
All-in-all the perl method seems more clean to me since the character to look for can be bundled into the square brackets; e.g., [ACGT]. But then I am mainly a Perl programmer.Comment
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Yes, I agree with westerman, Perl is also good. I found myself using a bit of Perl, awk, and sed everyday.
QComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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