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cbirdlab / dDocentHPC

hard fork of dDocent, edited to run without interactive user input
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Splitting BAM files for parallel freebayes #2

Open jdselwyn opened 4 years ago

jdselwyn commented 4 years ago

There appears to be a problem with how BAM files are concatenated and split prior to using freebayes. With the oyster mitochondrion bam files freebayes only called anything (including monomorphic sites) for the first ~ half of the sequence. When I simply ran in serial and fed a list of bamfiles to freebayes it called snps across the entire reference sequence.

cbird808 commented 4 years ago

I cannot reproduce this issue with my other datasets, but there was a problem with sort --parallel being used in the script but not on the hpc. The hpc has been updated with a parallel sort when you module load ddocent/2.7.8