MAQ and SNP calling
 

Hello,
I've used MAQ to call SNPs in Illumina data, it worked fine apart from the read depth. When I looked at the alignment using IGV the read depth is often alot more. Im sure theres a reason, can anyone tell me why?.

Thank you

Look at the default filtering: mapping quality etc. These may be reducing coverage (filtering reads) during SNP calling. This is a good thing, since poorly mapped reads or high-error reads may introduce artifacts.

can any one tell me the details regarding the alignment output of maq

Quote:

Originally Posted by bioenvisage (Post 11348) can any one tell me the details regarding the alignment output of maq

Well, the maq map output itself is binary. You can run the pileup command to give you the read bases and the quality at each position. Check the maq documentation and that should elaborate further what the columns in the output are.

BertieW