Hello,
I'm doing mutation detection by ~30x Illumina genome resequencing on a haploid eukaryote.
Maq seems to be working fine otherwise, not that I have a great deal of experience here, but final SNP list includes MASSES of ambiguous calls (ie. C>M, G>R etc) many with max phred of 255. By masses I mean ~2/3, from ~1700 total filtered SNPs over the genome. From a haploid! And this is randomly distributed over the entire genome, 8 chromosomes, so it's not partial duplications or restricted to repetitive sequence.
I should say I'm manually filtering to advised thresholds (phred 40, depth 3, also looking at neighbouring quality and number of hits but these numbers are looking fine) rather than running SNPfilter, but I don't think this should matter AFAIK. Mostly using default maq settings, except for the consensus assembly (-s -q 30).
I'm moving to BWA/SAMtools to compare, but still, anyone know what could be going on here? I'm very happy to just throw these away if spurious, but not without knowing why they're getting through.
Thanks,
Luke
I'm doing mutation detection by ~30x Illumina genome resequencing on a haploid eukaryote.
Maq seems to be working fine otherwise, not that I have a great deal of experience here, but final SNP list includes MASSES of ambiguous calls (ie. C>M, G>R etc) many with max phred of 255. By masses I mean ~2/3, from ~1700 total filtered SNPs over the genome. From a haploid! And this is randomly distributed over the entire genome, 8 chromosomes, so it's not partial duplications or restricted to repetitive sequence.
I should say I'm manually filtering to advised thresholds (phred 40, depth 3, also looking at neighbouring quality and number of hits but these numbers are looking fine) rather than running SNPfilter, but I don't think this should matter AFAIK. Mostly using default maq settings, except for the consensus assembly (-s -q 30).
I'm moving to BWA/SAMtools to compare, but still, anyone know what could be going on here? I'm very happy to just throw these away if spurious, but not without knowing why they're getting through.
Thanks,
Luke
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