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kspham / rnavariantcalling

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freebayes for rna-seq #9

Closed kspham closed 8 years ago

kspham commented 8 years ago

RNA-seq in some areas have very high coverage or very low coverage (very different from DNA). This causes the memory intensive scenario that we observed. We should subsample these high coverage regions before moving to freebayes.

ptdtan commented 8 years ago

I see. I'm trying to subsample those high coverage regions at the moment

ptdtan commented 8 years ago

Could you suggest any efficient method, Son?

ptdtan commented 8 years ago

Hmm, an issue which was reported on freebayes repository few days ago state that 1.0.1 version of freebayes cause memory leaking but the older version. I replaced current freebayes version by the older one then the memory problem was resolved.