I've been using Stampy to map Illumina reads and it's great. However I'd like to use it for 454 alignment too so as to get SAM output, which is a better match to our SNP calling pipelines than the 454HCDiffs and .tsvs generated by Newbler.
However, Stampy only manages to map about 48% of 310000 reads, as opposed to Newbler mapping over 85%.
Has anyone else tried to modify settings on Stampy to better map 454 data ? Or has any other recommendations for getting 454 data mapped in SAM format ?
cheers
Colin
However, Stampy only manages to map about 48% of 310000 reads, as opposed to Newbler mapping over 85%.
Has anyone else tried to modify settings on Stampy to better map 454 data ? Or has any other recommendations for getting 454 data mapped in SAM format ?
cheers
Colin
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