I have indexed a gzipped reference with bwa: bwa index reference.fa.gz
, which produces a series of other files reference.fa.gz.{amb,ann,bwt,pac,sa}
. These are working fine with bwa alignment.
I have discovered that samtools does not take a gzipped reference, so I am planning to use an unzipped version of the reference for my workflow instead of dealing with two separate representations of the reference.
Are the files reference.fa.gz.{amb,ann,bwt,pac,sa}
dependent upon the reference being gzipped? Do I need to reindex the unzipped reference.fa with bwa, or can I just rename the current files to remove the .gz
portion of the filename?