Human reference files in HG38 GATK resource bundle

Question

[win]

hi all, maybe i missed something obvious in the GATK resource bundle (cloud bucket) at the following site.

https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

they have this

Homo_sapiens_assembly38.fasta

file but it's

.sa

index file is missing. Whereas there is another file

Homo_sapiens_assembly38.fasta.64.sa

Is this the sa file for the alt reference assembly? If so why is the sa file for the main assembly not show?

which assembly is to be used for exome analysis?

thanks in advance.

[DareDevil]

Run samtools faidx Homo_sapiens_assembly38.fasta

[GenoMax]

Perhaps you just need to symlink Homo_sapiens_assembly38.fasta to Homo_sapiens_assembly38.fasta.64.

[Pierre Lindenbaum]

Hum... .what kind of 'index' do you expect ? samtools ? bwa ?

[win]

i was expecting bwa indices

[GenoMax]

The files with .64.sa/.ann/.bwt/.pac are the bwa index files.

[win]

So what is the significance of the .64 in the fasta file name?

[field654]

I had the same confusion. Why add .86? How is it different?