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Merged
merged 26 commits into from
Sep 2, 2025
Merged

Feature/pcgr v2.2.1 #10

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107a914
uptade docker image
qclayssen Apr 6, 2025
0ec6c09
chang command pcgr
qclayssen Apr 14, 2025
c51feda
change pcgr vcf header/info
qclayssen Apr 14, 2025
feace9f
uptade pcgr tier
qclayssen Apr 15, 2025
d21d145
remove in annotation cosmic and ICG un uptade variable name
qclayssen Apr 15, 2025
55f0f00
change filter remove COSMIC_COUN and ICGC_PCAWG and change name pcgr …
qclayssen Apr 15, 2025
f381589
change test
qclayssen Apr 15, 2025
642d691
add input vep dir for pcgr 2.2.1
qclayssen Jun 27, 2025
a7a36ea
update CPSR-related constants and file naming conventions for pcgr v2.1
qclayssen Jul 1, 2025
1611869
remove unused PCGR_ACTIONABILITY_TIER header entry and update TSV fil…
qclayssen Jul 1, 2025
64c3486
add back PCGR_ACTIONABILITY_TIER
qclayssen Jul 3, 2025
ecede4b
Allow missing pcgr annotation for somatic record
qclayssen Jul 21, 2025
33c4bf9
remove PCGR temp dir made for fusion we no longer use
qclayssen Jul 22, 2025
d7e0e73
creat pcgr output dir
qclayssen Jul 23, 2025
ef9fb08
update pcgr germline command
qclayssen Jun 27, 2025
9d695b3
change vep #fork to recommanded one "Number of forks that VEP can use…
qclayssen Jul 24, 2025
2e6c3ea
Fix I/O compress file and add logs
qclayssen Jul 17, 2025
94d4875
Add input variant filter for final PCGR report
Jan 22, 2025
d6e8b53
uptade pcgr tier
qclayssen Apr 15, 2025
59be8dc
update CPSR-related constants and file naming conventions for pcgr v2.1
qclayssen Jul 1, 2025
eb24836
linting
qclayssen Aug 28, 2025
5109ebb
Fix import
qclayssen Aug 28, 2025
a91ff86
remove dead code
qclayssen Aug 28, 2025
b0cfc8e
remove test assert absence `FILTER` column because now needed for bre…
qclayssen Aug 28, 2025
acb6862
Fix, update clinical potential rescue test
Aug 28, 2025
ced742e
Merge remote-tracking branch 'origin/release/0.3.0' into feature/pcgr…
qclayssen Aug 29, 2025
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78 changes: 32 additions & 46 deletions bolt/common/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,9 @@
'pathogenic',
'uncertain_significance',
}
PCGR_TIERS_RESCUE = {
'TIER_1',
'TIER_2',
PCGR_ACTIONABILITY_TIER_RESCUE = {
'1',
'2',
}


Expand Down Expand Up @@ -116,16 +116,14 @@ class VcfInfo(enum.Enum):
SAGE_NOVEL = 'SAGE_NOVEL'
SAGE_RESCUE = 'SAGE_RESCUE'

PCGR_TIER = 'PCGR_TIER'
PCGR_ACTIONABILITY_TIER = 'PCGR_ACTIONABILITY_TIER'
PCGR_CSQ = 'PCGR_CSQ'
PCGR_MUTATION_HOTSPOT = 'PCGR_MUTATION_HOTSPOT'
PCGR_CLINVAR_CLNSIG = 'PCGR_CLINVAR_CLNSIG'
PCGR_CLINVAR_CLASSIFICATION = 'PCGR_CLINVAR_CLASSIFICATION'
PCGR_COSMIC_COUNT = 'PCGR_COSMIC_COUNT'
PCGR_TCGA_PANCANCER_COUNT = 'PCGR_TCGA_PANCANCER_COUNT'
PCGR_ICGC_PCAWG_COUNT = 'PCGR_ICGC_PCAWG_COUNT'

CPSR_FINAL_CLASSIFICATION = 'CPSR_FINAL_CLASSIFICATION'
CPSR_PATHOGENICITY_SCORE = 'CPSR_PATHOGENICITY_SCORE'
CPSR_CLINVAR_CLASSIFICATION = 'CPSR_CLINVAR_CLASSIFICATION'
CPSR_CSQ = 'CPSR_CSQ'

Expand All @@ -151,7 +149,7 @@ class VcfInfo(enum.Enum):

GNOMAD_AF = 'gnomAD_AF'

PCGR_TIER_RESCUE = 'PCGR_TIER_RESCUE'
PCGR_ACTIONABILITY_TIER_RESCUE = 'PCGR_ACTIONABILITY_TIER_RESCUE'
SAGE_HOTSPOT_RESCUE = 'SAGE_HOTSPOT_RESCUE'
CLINICAL_POTENTIAL_RESCUE = 'CLINICAL_POTENTIAL_RESCUE'

Expand Down Expand Up @@ -270,7 +268,7 @@ def namespace(self):
'Description': 'Variant rescued by a matching SAGE call',
},

VcfInfo.PCGR_TIER: {
VcfInfo.PCGR_ACTIONABILITY_TIER: {
'Number': '1',
'Type': 'String',
'Description': (
Expand All @@ -281,28 +279,29 @@ def namespace(self):
},
VcfInfo.PCGR_CSQ: {
'Number': '.',
'Type': 'String',
'Description': (
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|'
'Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|'
'CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|'
'DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|'
'MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|'
'UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|'
'gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|'
'gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|'
'NearestExonJB'
),
'Type': 'String',
'Description': (
'Consequence annotations from Ensembl VEP. Format: '
'Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|'
'HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|'
'ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|'
'MANE|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|'
'UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|'
'gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|'
'gnomADe_REMAINING_AF|gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|'
'MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|'
'MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref'
),
},
VcfInfo.PCGR_MUTATION_HOTSPOT: {
'Number': '.',
'Type': 'String',
'Description': 'Known cancer mutation hotspot, as found in cancerhotspots.org_v2, Gene|Codon|Q-value',
'Description': 'Known cancer mutation hotspot, as found in cancerhotspots.org. Format: GeneSymbol|Entrez_ID|CodonRefAA|Alt_AA|Q-value',
},
VcfInfo.PCGR_CLINVAR_CLNSIG: {
VcfInfo.PCGR_CLINVAR_CLASSIFICATION: {
'Number': '.',
'Type': 'String',
'Description': 'ClinVar clinical significance',
'Description': 'ClinVar - clinical significance - per phenotype submission',
},
VcfInfo.PCGR_COSMIC_COUNT: {
'Number': '1',
Expand All @@ -320,23 +319,10 @@ def namespace(self):
'Description': 'Count of ICGC PCAWG hits',
},

VcfInfo.CPSR_FINAL_CLASSIFICATION: {
'Number': '1',
'Type': 'String',
'Description': (
'Final variant classification based on the combination of CLINVAR_CLASSIFICTION (for '
'ClinVar-classified variants), and CPSR_CLASSIFICATION (for novel variants)'
),
},
VcfInfo.CPSR_PATHOGENICITY_SCORE: {
'Number': '1',
'Type': 'Float',
'Description': 'Aggregated CPSR pathogenicity score',
},
VcfInfo.CPSR_CLINVAR_CLASSIFICATION: {
'Number': '1',
'Type': 'String',
'Description': 'Clinical significance of variant on a five-tiered scale',
'Description': 'ClinVar - Overall clinical significance of variant on a five-tiered scale',
},
VcfInfo.CPSR_CSQ: {
'Number': '.',
Expand All @@ -345,13 +331,13 @@ def namespace(self):
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|'
'Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|'
'Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|'
'FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE_SELECT|'
'MANE_PLUS_CLINICAL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|'
'DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF|gnomAD_AFR_AF|'
'gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|'
'gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|'
'MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|LoF|LoF_filter|LoF_flags|'
'LoF_info'
'FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|MANE_SELECT|'
'MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|'
'DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|'
'gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|gnomADe_REMAINING_AF|'
'gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|'
'MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|MaxEntScan_alt|MaxEntScan_diff|'
'MaxEntScan_ref'
),
},

Expand All @@ -360,7 +346,7 @@ def namespace(self):
'Type': 'Flag',
'Description': '',
},
VcfInfo.PCGR_TIER_RESCUE: {
VcfInfo.PCGR_ACTIONABILITY_TIER_RESCUE: {
'Number': '0',
'Type': 'Flag',
'Description': '',
Expand Down
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