How to detect homozygous SNPs with GigaBayes

[fikys]

I have hard time finding SNPs that are homozygous in all 454 reads when compared to the reference sequence (the reference sequence will have the second allele) from MosaikAligner assembly using GigaBayes software. It always reports only those SNPs that are represented by different alleles in the reads:

AAGTTT - reference (1)

AAGTTT
AAGTTT
AACTTT
AACTTT
(G/C) will be reported


AAGTTT - reference (2)

AACTTT
AACTTT
AACTTT
AACTTT

(G/C) will not be reported

I'm using --anchor option to use the reference to call a SNP but it seems still ignoring second type of SNPs.

Can anybody help?

[Saffron]

Hi,

I am having the same issue - did you figure out a solution to this?

Thanks.

Saffron

[fikys]

Yes, in my case it seem to be conflicting with the fact that I asked for 2X coverage of each allele... could not imagine that this will be applied to the reference sequence allele. These options produced homozygous SNPs together with low-quality heterozygous ones. Had to do a lot of additional filtering of GigaBayes output. I had two individuals that I compared to the same reference sequence.

Command line that generated this output: gigaBayes --gig ./pyrobase/assembly_sen/chr1.gig --sample multiple --sampleDel F --ploidy diploid --anchor --O 4 --CRL 3 --CRU 31 --gff ./pyrobase/chr1.gff