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Create pVACsplice wdl on analysis wdl

My Hoang edited this page Dec 19, 2024 · 3 revisions

To-do:

  1. create analysis-wdls/definitions/tools/regtools.wdl
  2. create analysis-wdls/definitions/tools/pvacsplice.wdl
  3. create analysis-wdls/definitions/subworkflows/pvacsplice.wdl
Compare pvacseq and pvacsplice inputs
+ pvacseq: 
a) annotated vcf (require WT, frameshift pluggin)
b) phased vcf

+ pvacsplice : 
a) annotated vcf (doesnt require frameshift pluggin)
b) regtools tsv
c) reference fasta 
d) reference gtf

Both require MHC alleles

pvacsplice (vs pvacseq):

  • requires reference fasta (reference dna fasta, not to be confused with peptide_fasta)
  • requires reference gtf
  • requires regtools tsv (splice variants, splice sites, read counts for splice variants)
  • doesnt predict MHC anchor location (since there's no matched WT)
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