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.
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.