realign to deambig in denovo #17
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attempt to fix error "Input files reads and reference have incompatible contigs." related to consensus calling (w/GATK) on a reference genome that was not the exact same fasta that was used to align against; align the reads to the randomly imputed ref instead of the ambig ref.
dpark01
approved these changes
Oct 1, 2020
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This is an attempt to fix the GATK error
Input files reads and reference have incompatible contigs.related to consensus calling (w/GATK) on a reference genome that was not the exact same fasta that was used to align against; with these changes the reads are aligned to the randomly imputed ref instead of the ambig ref.