During the annotation of the TCGA I ran into a couple of bugs/problems:
The queries to the allele registry would sometimes time out/hit the default retry limit, especially for larger files. This updates the number of retries to 5 and implements a backoff factor.
Some chromosomes are not supported (e.g. M) and would throw an error in the _refseq_sequence_b38 method
GRCh38 uses the chr prefix, which we didn't handle.
During the annotation of the TCGA I ran into a couple of bugs/problems:
_refseq_sequence_b38methodchrprefix, which we didn't handle.