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📝 Update SNV Annot Ref #19

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Jul 18, 2024
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📝 Update SNV Annot Ref #19

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2 changes: 1 addition & 1 deletion docs/SOMATIC_SNV_ANNOT_README.md
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Expand Up @@ -44,7 +44,7 @@ Secondary files needed for each reference file will be a sub-bullet point
- `gatk_filter_expression`: ["vc.getGenotype('insert_normal_sample_name').getDP() <= 7", "gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER=='PASS'"] # NOTE!! Replace `insert_normal_sample_name` with the value you'd use for `input_normal_name`! # NOTE!! If your annotation includes dot values, those values must first be excluded! If they are not, GATK will error trying to convert those values!
- `vep_cache`: `homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz`
- `genomic_hotspots`: `tert.bed` # This file has two common TERT promoter gene hot spots
- `protein_snv_hotspots`: `protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted SNV + MNV subset of https://www.cancerhotspots.org/files/hotspots_v2.xls
- `protein_snv_hotspots`: `kfdrc_protein_snv_cancer_hotspots_20240718.txt` # Column-name-containing, tab-delimited file(s) containing protein names and amino acid positions corresponding to hotspots. File header contains generation history
- `protein_indel_hotspots`: `protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted INDEL subset of https://www.cancerhotspots.org/files/hotspots_v2.xls
- `custom_enst`: `kf_isoform_override.tsv` # As of VEP 104, several genes have had their canonical transcripts redefined. While the VCF will have all possible isoforms, this affects maf file output and may results in representative protein changes that defy historical expectations

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4 changes: 2 additions & 2 deletions workflows/kfdrc-somatic-snv-annot-workflow.cwl
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Expand Up @@ -49,7 +49,7 @@ doc: |
- `gatk_filter_expression`: ["vc.getGenotype('insert_normal_sample_name').getDP() <= 7", "gnomad_3_1_1_AF != '.' && gnomad_3_1_1_AF > 0.001 && gnomad_3_1_1_FILTER=='PASS'"] # NOTE!! Replace `insert_normal_sample_name` with the value you'd use for `input_normal_name`! # NOTE!! If your annotation includes dot values, those values must first be excluded! If they are not, GATK will error trying to convert those values!
- `vep_cache`: `homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz`
- `genomic_hotspots`: `tert.bed` # This file has two common TERT promoter gene hot spots
- `protein_snv_hotspots`: `protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted SNV + MNV subset of https://www.cancerhotspots.org/files/hotspots_v2.xls
- `protein_snv_hotspots`: `kfdrc_protein_snv_cancer_hotspots_20240718.txt` # A text formatted SNV + MNV version of https://www.cancerhotspots.org/files/hotspots_v2.xls. See file header for details
- `protein_indel_hotspots`: `protein_indel_cancer_hotspots_v2.ENS105_liftover.tsv` # A tsv formatted INDEL subset of https://www.cancerhotspots.org/files/hotspots_v2.xls
- `custom_enst`: `kf_isoform_override.tsv` # As of VEP 104, several genes have had their canonical transcripts redefined. While the VCF will have all possible isoforms, this affects maf file output and may results in representative protein changes that defy historical expectations

Expand Down Expand Up @@ -146,7 +146,7 @@ inputs:
class: File, path: 607713829360f10e3982a423, name: tert.bed}]}
protein_snv_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited
file(s) containing protein names and amino acid positions corresponding to hotspots",
"sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6a, name: protein_snv_cancer_hotspots_v2.ENS105_liftover.tsv}]}
"sbg:suggestedValue": [{class: File, path: 66980e845a58091951d53984, name: kfdrc_protein_snv_cancer_hotspots_20240718.txt}]}
protein_indel_hotspots: {type: 'File[]?', doc: "Column-name-containing, tab-delimited
file(s) containing protein names and amino acid position ranges corresponding
to hotspots", "sbg:suggestedValue": [{class: File, path: 663d2bcc27374715fccd8c6f,
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