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lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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Update bwakit release #189

Open godotgildor opened 6 years ago

godotgildor commented 6 years ago

Hi Heng, I'm trying to generate the hs38DH genome using the script in bwakit. If I use the data in the github repo, the necessary resources folder with the HLA and decoy sequence fasta isn't present. However, the latest bwakit release on sourceforge is for 0.7.15, and the script in that version points to an older and now non-functioning URL for the main fasta. Is there somewhere to grab 0.7.17 with the resources folder? Alternatively, is it safe to grab the resources folder from 0.7.15 and use it with the script in bwakit 0.7.17?

jfass commented 5 years ago

Just came across this myself: change the line in the "run-gen-ref" script that says:

url38="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz

So that it says:

url38="ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz