update IPAW to hg38 genome

[yafeng]

The current IPAW pipeline utilises hg19 genome based databases, and the reported coordinates of novel peptides and SAAV peptides are hg19 genomic coordinates. The goal is to make IPAW compatible for latest hg38 genome assembly.

[yafeng]

1. Find corresponding hg38 resources - conservation bigWig files.

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons100way/hg38.phastCons100way.bw

https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF+1.bw
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF+2.bw
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF+3.bw
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF-1.bw
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF-2.bw
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg38/latest/PhyloCSF-3.bw

[yafeng]

2. COSMIC and dbSNP in hg38 version
   Get the SNP database
   https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=682621893_rZAeDI3qkmv2ea9OULNeBo6GjEui&clade=mammal&org=&db=hg38&hgta_group=varRep&hgta_track=snp150Common&hgta_table=snp150CodingDbSnp&hgta_regionType=genome&position=&hgta_outputType=primaryTable&hgta_outFileName=snp150CodingDbSnp.txt

Get the COSMIC database
sftp 'your_email_address@example.com'@sftp-cancer.sanger.ac.uk
Download the data

sftp> get cosmic/grch38/cosmic/v85/CosmicMutantExport.tsv.gz
sftp> exit

[yafeng]

3. Get the hg38 masked genome sequence

wget hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFaMasked.tar.gz
tar hg38.chromFaMasked.tar.gz
for chr in {1..22} X Y M; do cat chr$chr.fa.masked >> hg38.chr1-22.X.Y.M.fa.masked; done

[yafeng]

4. varDB 2.0 database with latest pseudogene, lncRNA, nsSNPs and COSMIC DB
   aiming to include:
   a. GENCODE release 28 pseudogenes including consensus pseudogenes predicted by the Yale and UCSC pipelines
   b. lncRNAs from LNCipedia v5.1 (hg38)
   c. mutant peptides derived from somatic mutations in COSMIC v85
   d. mutant peptides derived from nsSNPs in dbSNP150

[yafeng]

varDB2.0 database can be downloaded from:
wget http://lehtiolab.se/Supplementary_Files/VarDB2.zip

[yafeng]

Add a command-line option --hg19 or --hg38 so that the workflow can be run under different genome assembly. The following processes need to be modified accordingly:
BLATnovel, phastcons, phyloCSF , annovar

[yafeng]

I made a copy of ipaw for hg38 genome.
https://github.com/yafeng/proteogenomics-analysis-workflow/commit/839f18545053145ffca8b36723811f691beb6578

[TnakaNY]

Could you provide a copy of ipaw for hg38 genome?
Or, latest version is for hg38?

[TnakaNY]

Hi Yafeng,

Could you please also upload varDB2.0 anywhere?
I could not download by using your suggestion above.

Thx.

[yafeng]

@TnakaNY
try this link for VarDB2.0
https://drive.google.com/open?id=1G20qIF60xdJ5zrSbt8a8sd0RKutYxQMC

you need to use ipaw hg38 version, which I uploaded under my github repo. And you need to use conda to set up local environments so that all executive commands can be found. It take some efforts to set up. Otherwise, I suggest you continue to use hg19, which is better maintained.

https://github.com/yafeng/proteogenomics-analysis-workflow/blob/master/ipaw.local.hg38.nf

[TnakaNY]

Thank you, let me try!