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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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Correct handling of genotype info when outputting results in YAML mode #460

Closed justaddcoffee closed 4 years ago

justaddcoffee commented 4 years ago

Addresses https://github.com/TheJacksonLaboratory/LIRICAL/issues/459 - in YAML mode, tsv/html templates were ignoring genotype info, even when phenotypeOnly was false and genotype info was present.

pnrobinson commented 4 years ago

This seems to be a partial fix. When I run with this yml:

## LIRICAL Analysis Template.
# These are all the possible options for running LIRICAL. Use this as a template for
# your own set-up.
---
analysis:
  # hg19 or hg38 is supported
  genomeAssembly: hg19
  #vcf: /path/to/Pfeiffer.vcf
  vcf: /home/robinp/data/lirical/project.NIST.hc.snps.indels.NIST7035.vcf
  #exomiser: /path/to/1802_hg19/
  exomiser: /home/robinp/data/exomiserdata/1902_hg19
  transcriptdb: refseq
#hpoIds: ['HP:0001156', 'HP:0001363', 'HP:0011304', 'HP:0010055']
hpoIds: ['HP:0001875', 'HP:0001888', 'HP:0001973', 'HP:0002014', 'HP:0002024', 'HP:0002650', 'HP:0003765', 'HP:0004389', 'HP:0006532', 'HP:0007131', 'HP:0011108', 'HP:0100825']
prefix: P0001721_lirical

then I do not seem the error, but the genotype information is not used or not displayed.

justaddcoffee commented 4 years ago

Thanks Peter, will rerun and check with your yaml file

justaddcoffee commented 4 years ago

I can't reproduce your lack of genotype info using this YAML using the Pfeiffer vcf. I'm seeing fgfr2 genotype info displayed:

Could you send me your project.NIST.hc.snps.indels.NIST7035.vcf? Are we sure any genotype info should be displayed for this vcf?