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?
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?
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