maq-0.7.1 12-column cns.snp files?

[elaney_k]

Hi,

I've recently downloaded and started running maq-0.7.1 instead of maq-0.6.6. All input files are the same however when i run cns2snp on it's own or through the easyrun script program i get a 12-column output file instead of the usual 9-column file, has anyone else found this or know why this happens?

(I've also tried running the maq.pl demo command with the same result)

Example of output:
chr1 27077 G K 204 119 1 63 62 G 71 T
chr1 27126 T Y 219 141 1 63 62 T 99 C
chr1 27754 C Y 232 139 1 61 62 C 67 T

Many thanks for any help you can give me,

Elaine

[ptongyoo]

I never use the 0.6.6 version before. I also used 0.7.1 and in the manual of 0.7.1 describe this

"Extract SNP sites. Each line consists of chromosome, position, reference base, consensus base, Phred-like consensus quality, read depth, the average number of hits of reads covering this position, the highest mapping quality of the reads covering the position, the minimum consensus quality in the 3bp flanking regions at each side of the site (6bp in total), the second best call, log likelihood ratio of the second best and the third best call, and the third best call."

Cheers.

[elaney_k]

Hi,

That's exactly the info I was looking for, thank-you! Can you tell me where you downloaded the manual from with this information as the maq.pdf file that comes with the download (maq-0.7.1 2008-09-22 ) only gives the information for the first 9 columns.

Many thanks for your reply,

Elaine