Requires 'chr' for contig names in all analyses? about hap.py

[brendanofallon]

I realize now that a potential workaround is to specify --no-fixchr-truth and --no-fixchr-query and -l [list of contig names], which seems to work for me. A little cumbersome, perhaps, but workable ;)

[pkrusche]

Yes, I actually have a ticket for version 0.2.8 to make this easier.

The reason for the current behaviour is to simplify switching between hg19 (which has chr prefixes) and GRCH37 (which doesn't). For the purposes of Platinum Genomes comparisons (which are done on chr1-22), these two are equivalent.

If neither test_input.vcf.gz nor test_calls.vcf.gz contain contigs with a chr prefix, hap.py should automatically decide to not change the chromosome prefix however. If it still does, then this is a bug.

[pkrusche]

Version 0.2.8 detects numeric chromosome names from the reference fasta file, so the switches above should not be necessary anymore.