64 bit index breaks alt aware alignment.

[shawarden]

If you have a 64 bit system, binary and index file set but no matching reference.fasta.64.alt file (say only a reference.fasta.alt that comes from run-gen-ref) then bwa will not run as alt-aware.

While you can just copy/softlink the reference.fasta.alt to reference.fasta.64.alt to fix this, it might be better to remove the .64 from the .alt file's path since the .alt file is not created by the index command and thus should not be pathed with other files that are.

[mmokrejs]

Where does the '64.' come from? Is that your invention how you name the files?

Ah, I see:

Usage:   bwa index [options] <in.fasta>

Options: -a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]
         -p STR    prefix of the index [same as fasta name]
         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.*

I was about to report that ALT index is not found in the following scenario if you use as the reference *.fasta.gz and the ALT index is just *.fasta.alt:

Let's say you have these two files (bwa can use either as the reference, but the question is qhich of them did you index and for which you provided the ALT index file: $file.fasta.gz $file.fasta

bwa index $file.fasta.gz
cp /elsewhere/grch38.fa.alt $file.fasta.alt
bwa mem -t 16 -p -M $file.fasta.gz reads.fastq