Olamide Isreal
9e6a16c19b
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
32 lines
673 B
INI
32 lines
673 B
INI
cache 1
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dir_cache /data
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assembly 'GRCh38'
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offline 1
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force_overwrite 1
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custom file=/opt/vep/.vep/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz,short_name=COSMIC,format=vcf,type=exact,fields=LEGACY_ID%CNT
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# Functional impact predictions
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sift b # CALCULATE 1 - score
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polyphen b # THESE TWO CAN BE AVERAGED
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plugin REVEL,/opt/vep/.vep/REVEL/new_tabbed_revel_grch38.tsv.gz
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# TODO: CALCUALTE THEIR L2 NORM
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# plugin CADD,/opt/vep/.vep/CADD/GRCh38/whole_genome_SNVs.tsv.gz,/opt/vep/.vep/CADD/GRCh38/InDels.tsv.gz
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# Clinical significance
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check_existing
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clinvar
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# Allele frequencies
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af
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af_1kg
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af_gnomade
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af_gnomadg
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max_af
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# Additional useful flags
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numbers
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hgvs
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symbol
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canonical |