I just pulled the newest development branch and packed it with maven. I also used the

VCF-File: <div class="snippet-clipboard-content notranslate position-relative over

On Mon, Feb 9, 2015 at 5:13 PM, Jules Jacobsen <a href="mailto:notifications@github.co

Fail to run --prioritiser phenix about exomiser HOT 10 CLOSED

visze commented on June 9, 2024

Fail to run --prioritiser phenix

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Comments (10)

visze commented on June 9, 2024

VCF-File:

##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[rmdup.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/parkhomc/reference/hg19/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 enable_experimental_downsampling=false baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=30 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.05 logRemovedReadsFromContaminationFiltering=null exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=1,length=249250621,assembly=b37>
##contig=<ID=2,length=243199373,assembly=b37>
##contig=<ID=3,length=198022430,assembly=b37>
##contig=<ID=4,length=191154276,assembly=b37>
##contig=<ID=5,length=180915260,assembly=b37>
##contig=<ID=6,length=171115067,assembly=b37>
##contig=<ID=7,length=159138663,assembly=b37>
##contig=<ID=8,length=146364022,assembly=b37>
##contig=<ID=9,length=141213431,assembly=b37>
##contig=<ID=10,length=135534747,assembly=b37>
##contig=<ID=11,length=135006516,assembly=b37>
##contig=<ID=12,length=133851895,assembly=b37>
##contig=<ID=13,length=115169878,assembly=b37>
##contig=<ID=14,length=107349540,assembly=b37>
##contig=<ID=15,length=102531392,assembly=b37>
##contig=<ID=16,length=90354753,assembly=b37>
##contig=<ID=17,length=81195210,assembly=b37>
##contig=<ID=18,length=78077248,assembly=b37>
##contig=<ID=19,length=59128983,assembly=b37>
##contig=<ID=20,length=63025520,assembly=b37>
##contig=<ID=21,length=48129895,assembly=b37>
##contig=<ID=22,length=51304566,assembly=b37>
##contig=<ID=X,length=155270560,assembly=b37>
##contig=<ID=Y,length=59373566,assembly=b37>
##contig=<ID=MT,length=16569,assembly=b37>
##reference=file:hg19/human_g1k_v37.fasta
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  father  mother  child
12  40646739    rs200920379 C   T   2008.77 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.351;DP=146;Dels=0.00;FS=7.130;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=1.826;QD=13.76;ReadPosRankSum=0.417  GT:AD:DP:GQ:PL  0/1:74,72:131:99:2037,0,2104    0/0:131,0:131:99:2037,0,2104    0/1:74,72:131:99:2037,0,2104
12  40646760    rs376621322 A   C   1932.77 .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.124;DP=135;Dels=0.00;FS=3.727;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=0.530;QD=14.32;ReadPosRankSum=0.583  GT:AD:DP:GQ:PL  0/0:122,0:122:99:1961,0,1835    0/1:68,67:122:99:1961,0,1835    0/1:68,67:122:99:1961,0,1835
12  40646786    rs34594498  C   T   375.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.017;DP=34;Dels=0.00;FS=7.846;HaplotypeScore=15.1246;MLEAC=1;MLEAF=0.500;MQ=70.00;MQ0=0;MQRankSum=-0.638;QD=11.05;ReadPosRankSum=-0.190    GT:AD:DP:GQ:PL  0/1:18,16:31:99:404,0,477   ./.:18,16:31:99:404,0,477   ./.:18,16:31:99:404,0,477

Ped-File:

fam1 father 0      0       1 1
fam1 mother 0      0       2 1
fam1 child father mother  1 2

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julesjacobsen commented on June 9, 2024

Hi Max,

Thanks for the detailed bug-report and sorry this took a while. This is an 'oddity' (I guess it's a bug really) with phenix. Phenix expects HPO terms as an input, which you didn't give. Instead you gave a disease id of some sort. If you replace your -D 607060 option with --hpo-terms=HP:0000510 you should find that it will run.

Did you expect that the disease id would be converted into HPO ids?

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visze commented on June 9, 2024

Hi Jules,

yes I expected that it will use the HPO terms associated with the OMIM id.

The error message is really confusing. It gives the impression that some files are missing. Maybe we should add a better error. Like: Please insert HPO terms for method phenix.

Or convert the OMIM-ID to HPO-terms.

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julesjacobsen commented on June 9, 2024

OK, I had the exact same error once and was similarly confused with the error message. We already do conversion of the disease id to HPO terms (You need to have a database identifier e.g. OMIM: as we also have ORPHANET: so a number isn't descriptive enough) , and having just a list of HPO terms is clear enough, but what would you expect if you used --disease-id and --hpo-terms? Include them all in one superset and analyse on that?

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damiansm commented on June 9, 2024

On Mon, Feb 9, 2015 at 5:13 PM, Jules Jacobsen [email protected]
wrote:

OK, I had the exact same error once and was similarly confused with the
error message. We already do conversion of the disease id to HPO terms (You
need to have a database identifier e.g. OMIM: as we also have ORPHANET: so
a number isn't descriptive enough) , and having just a list of HPO terms is
clear enough, but what would you expect if you used --disease-id and
--hpo-terms? Include them all in one superset and analyse on that?

There is probably no right answer to that one. Really it is just use one or
the other i.e. use --disease-id if you are lazy or don't know the precise
patient phenotypes, otherwise use --hpo-terms.

Current behaviour in hiPHIVE is --hpo-terms overrides --disease-id if both
are specified and may just be easier to keep it that way round in terms of
my future benchmarking scripts!

—
Reply to this email directly or view it on GitHub
#37 (comment).

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visze commented on June 9, 2024

Jules, you're right. I forgot to add OMIM:

But I think we should unify the behavior of --disease-id and --hpo-terms for PHIVE, hiPHIVE and phenix. It will rise the usability and acceptance.

Disable the tag --disease-id when you insert --hpo-terms will be one possibility. Also we can only allow one of the tags. Otherwise we see an error with an info message: Please use --hpo-terms or --disease-id. Another possibility is to add the HPO-Terms of the disease to the --hpo-terms.

The best way to find it out is to ask clinicians which scenario they have. Maybe they like to combine diseases with phenotypes. Or maybe not. I can only guess.

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pnrobinson commented on June 9, 2024

I would tend to agree. There is currently no valid usage scenario where you would use botbh a disease and a set of HPO terms, so the exomiser should emit an error warning and quit if both flags are used. For the Website, the HPO terms should take precedence of the disease terms, but optimally an error window, perhaps a javascript widget, should pop up.
-cheers Peter

Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universit�t Berlin
Institut f�r Medizinische Genetik und Humangenetik
Charit� - Universit�tsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
[email protected]
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson

Von: Max [[email protected]]
Gesendet: Dienstag, 10. Februar 2015 09:44
An: exomiser/Exomiser
Betreff: Re: [Exomiser] Fail to run --prioritiser phenix (#37)

Jules, you're right. I forgot to add OMIM:

But I think we should unify the behavior of --disease-id and --hpo-terms for PHIVE, hiPHIVE and phenix. It will rise the usability and acceptance.

The best way to find it out is to ask clinicians which scenario they have. Maybe they like to combine diseases with phenotypes. Or maybe not. I can only guess.

�
Reply to this email directly or view it on GitHubhttps://github.com//issues/37#issuecomment-73663323.

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damiansm commented on June 9, 2024

My vote would be HPO terms takes precedence over disease but rather than
quitting the command-line and possibly the website should just issue a
warning to say the disease has been ignored?

On Tue, Feb 10, 2015 at 9:06 AM, Peter Robinson [email protected]
wrote:

I would tend to agree. There is currently no valid usage scenario where
you would use botbh a disease and a set of HPO terms, so the exomiser
should emit an error warning and quit if both flags are used. For the
Website, the HPO terms should take precedence of the disease terms, but
optimally an error window, perhaps a javascript widget, should pop up.
-cheers Peter

Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics
and Computer Science of the Freie Universit�t Berlin
Institut f�r Medizinische Genetik und Humangenetik
Charit� - Universit�tsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
[email protected]
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies:
http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson

Von: Max [[email protected]]
Gesendet: Dienstag, 10. Februar 2015 09:44
An: exomiser/Exomiser
Betreff: Re: [Exomiser] Fail to run --prioritiser phenix (#37)

Jules, you're right. I forgot to add OMIM:

But I think we should unify the behavior of --disease-id and --hpo-terms
for PHIVE, hiPHIVE and phenix. It will rise the usability and acceptance.

Disable the tag --disease-id when you insert --hpo-terms will be one
possibility. Also we can only allow one of the tags. Otherwise we see an
error with an info message: Please use --hpo-terms or --disease-id. Another
possibility is to add the HPO-Terms of the disease to the --hpo-terms.

The best way to find it out is to ask clinicians which scenario they have.
Maybe they like to combine diseases with phenotypes. Or maybe not. I can
only guess.

�
Reply to this email directly or view it on GitHub<
https://github.com/exomiser/Exomiser/issues/37#issuecomment-73663323>.

—
Reply to this email directly or view it on GitHub
#37 (comment).

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julesjacobsen commented on June 9, 2024

OK - well this has evolved to a different issue. I'm opening a new one to address the discussion - see issue #48.

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julesjacobsen commented on June 9, 2024

Closing this issue as this has been split into two child issues.

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Fail to run --prioritiser phenix about exomiser HOT 10 CLOSED

Comments (10)

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