I would like to obtain hg19 exome as a fasta file. I couldn't find something obvious about this here: ftp://ftp.broadinstitute.org/bundle/2.8/hg19/
Thanks in advance.
Why do you need the hg19 exome as a fasta file? You should be able to use the whole genome fasta file for mapping, then restrict the rest of your analysis to the exome intervals using -L.
Why I need the hg19 exome as fasta file - I am trying to replicate the IMPACT pipeline described by the authors here: http://tanlab.ucdenver.edu/IMPACT/IMPACT_USER_MANUAL_12172015.pdf http://tanlab.ucdenver.edu/IMPACT/
I got in touch with the author who mentioned that the relevant file was obtained from GATK. My assumption is that this file is the hg19 Exome as a fasta dump.
No, we don't provide exome fasta files, just the whole genome fasta
I think the best thing is to use -L as I recommended above.