Question: Human reference files in HG38 GATK resource bundle
0
gravatar for win
14 months ago by
win810
India
win810 wrote:

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.

vcf • 1.3k views
ADD COMMENTlink written 14 months ago by win810

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

ADD REPLYlink written 14 months ago by genomax65k

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

ADD REPLYlink written 14 months ago by Pierre Lindenbaum119k

i was expecting bwa indices

ADD REPLYlink written 14 months ago by win810

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

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax65k

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

ADD REPLYlink written 14 months ago by win810
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