Comments (4)
I believe those files were generated for the purposes of our pvacviz online demo and got uploaded to genomedata.org for book keeping purposes. They are generated from the same data (HCC1395) as used in the tutorials on pmbio.org. I think pmbio.org specifies the steps up to obtaining a vep annotated somatic vcf (Modules01-05) as well as obtaining expression data (Module-06). The coverage and expression data can then be added to the somatic vcf using the steps specified at https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep.html.
As for the phased vcf, the input data can also be downloaded from pmbio.org and the steps I followed to generate the annotated.phase.vcf.gz are here: https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/proximal_vcf.html.
Unfortunately, the workflow currently described at https://pmbio.org/module-08-immune/0008/02/01/Personalized_Cancer_Vaccine_Design/ focuses on getting the appropriate AWS setup to run pvactools but assumes you have a proper vcf generated prior to following those steps. Until we have that updated, the steps I outlined should be able to get you started on generating those files. Let me know if you run into any further issues.
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I'm not familiar with those files or how they were generated. They might be related to this tutorial: https://pmbio.org/module-08-immune/0008/01/01/Intro_to_Immunogenomic_Analysis/ although I don't see any instructions on how precisely they were generated. My best guess is that they were generate following all of the upstream steps in the different pmbio.org courses.
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I think @huimingx knows the most about this module of the PMBIO course. Is that what you are attempting to follow @ne1al ?
If so, this issue would probably make more sense posted to that repo: https://github.com/griffithlab/pmbio.org
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@malachig @susannasiebert @huimingx Thank you very much for your help and yes I was trying to follow a certain tutorial to regenerate those two vcf files. I appreciate your help. I will take a look at the resources you provided too
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Related Issues (20)
- Annotation VCF HOT 1
- Enhancement: Adding allele counts per strand in vcf-readcount-annotator HOT 1
- warn when pick flag is expected but not observed
- Add feature to vcf-genotype-annotator to allow for adding GT field to existing samples
- Inaccurate warning message when running vcf-expression-annotator
- Bug in "vcf-genotype-annotator" due to misspelling HOT 1
- vcf-readcount-annotator only annotates first variant for indel HOT 1
- getting error when The INFO field name to use HOT 4
- When running the vcf-info-annotator support input TSVs with multiple value columns
- AttributeError: 'bool' object has no attribute 'split' HOT 2
- vep_annotation_reporter.py + AttributeError: 'bool' object has no attribute 'split' HOT 3
- ref_transcript_mismatch_reporter: `ValueError: invalid literal for int() with base 10: '71/98'`
- VAtools vcf-expression-annotator does not add gene expression for genes without annotated gene names HOT 2
- small special bug about logging
- Installation via pip requires version previous than 21 because of Python version HOT 2
- vcf-readcount-annotator HOT 3
- VEP entry for at CHR chr*, POS *, REF *, ALT * already exists HOT 2
- ValueError: invalid literal for int() with base 10 HOT 1
- Support for GZ compressed annotation files
- Please consider adding support for multi-thread support HOT 3
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