Most genes have a single sequence in the primary contigs for Grch38. Should we mask these? This way reads will no longer be biased towards a primary alignment in the primary contigs, even when the Grch38 seq is worse, and will all align to the provided alt contigs.
Most genes have a single sequence in the primary contigs for Grch38. Should we mask these? This way reads will no longer be biased towards a primary alignment in the primary contigs, even when the Grch38 seq is worse, and will all align to the provided alt contigs.