Closed justaddcoffee closed 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.
Thanks Peter, will rerun and check with your yaml file
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?
Addresses https://github.com/TheJacksonLaboratory/LIRICAL/issues/459 - in YAML mode, tsv/html templates were ignoring genotype info, even when
phenotypeOnly
wasfalse
and genotype info was present.