MAQ and indel detection

[fadista]

I am using solexa paired-end data and after I mapped my reads to a reference sample with the MAQ software a message appears on the screen:
"[maq_indel_pe] the indel detector only works with short-insert mate-pair reads".
I am working with fragment sizes that have an average length of 315 bp and in the parameters -a and -A of the 'match' function I put the number 350.

My question is what does this message mean and am I not able to detect indels and, if not, why is that?


Best regards,
João Fadista

[zee]

Hi.

I've seen that message with single-end read alignments i.e.

maq out.map chr.bfa read1.bfq

So perhaps it's assuming that you didnt submit the other read2.bfq mate-pair file.