It would be great if the Alt contigs approach could be extended so SNAP could use two haplotype FASTA files with all chromosomes/contigs and assign better mapping qualities to reads that map to "multiple" places with the same score, but only once in each hapoltype.
It would be great if the
Alt contigsapproach could be extended so SNAP could use two haplotype FASTA files with all chromosomes/contigs and assign better mapping qualities to reads that map to "multiple" places with the same score, but only once in each hapoltype.