Human reference files in HG38 GATK resource bundle
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.
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Perhaps you just need to symlink
Homo_sapiens_assembly38.fastatoHomo_sapiens_assembly38.fasta.64.Hum... .what kind of 'index' do you expect ? samtools ? bwa ?
i was expecting bwa indices
The files with
.64.sa/.ann/.bwt/.pacare the bwa index files.So what is the significance of the .64 in the fasta file name?
I had the same confusion. Why add .86? How is it different?
Run
samtools faidx Homo_sapiens_assembly38.fasta