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.
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.