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Create pVACsplice wdl on analysis wdl
My Hoang edited this page Dec 19, 2024
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3 revisions
To-do:
- create analysis-wdls/definitions/tools/regtools.wdl
- create analysis-wdls/definitions/tools/pvacsplice.wdl
- 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)