MAQ for SNP genotyping

[phatjoe]

Hi,

I am new to MAQ and have a few questions on the aligner.

1. I have a trimmed paired-end shortreads with length that range between 45-90bp in a file. MAQ seemed to not be able to map for PE reads with different length? I got the following error:-

maq: read.cc:61: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strncmp(name, lr->name[j], tl-1) == 0' failed.

maq: read.cc:58: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `l >= size_r' failed.

In the manual, it says that I would have to use maq mapmerge for it? Does it mean that I would have to filter out reads of the same length and re-merge it?

In this case, does the different read lengths affect the mapping quality?

2. My other question is pertaining the read depth in the cns2snp file.

Reference A
============
contigs T
T
A
A
A
A
A
A
In the cns2snp file, the read depth reported is 8, the SNP that was called is A(reference) T (Alternate), instead of reporting an SNP coverage of 2. I understand that we can use SNPfilter to filter based on read depth and quality. But how do you go about this when the SNP coverage is relatively lower but the quality is >30?

Thanks!