@@ -11,19 +11,25 @@ below.
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CAPICE can be used as online service at http://molgenis.org/capice
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## Requirements
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- * VEP v107
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+ The list below is a complete list. Depending on whether GRCh37 and/or GRCh38 is used and whether all
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+ mentioned features are used, some items in the list below can be skipped.
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+
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+ * VEP v107
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+ * Including VEP cache (which needs to be unarchived!):
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+ * [ homo_sapiens_refseq_vep_107_GRCh37] ( http://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_refseq_vep_107_GRCh37.tar.gz )
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+ * [ homo_sapiens_refseq_vep_107_GRCh38] ( http://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_refseq_vep_107_GRCh38.tar.gz )
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* Including plugin(s):
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* [ Grantham] ( https://github.com/molgenis/vip/blob/master/resources/vep/plugins/Grantham.pm )
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* [ SpliceAI] ( https://github.com/molgenis/vip/blob/master/resources/vep/plugins/SpliceAI.pm )
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- * Including data (GRCh37) [ available here] ( https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/ ) :
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+ * Including additional data (GRCh37) [ available here] ( https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/ ) :
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* ` gnomad.total.r2.1.1.sites.stripped.vcf.gz `
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* ` gnomad.total.r2.1.1.sites.stripped.vcf.gz.csi `
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* ` hg19.100way.phyloP100way.bw `
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* ` spliceai_scores.masked.indel.hg19.vcf.gz `
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* ` spliceai_scores.masked.indel.hg19.vcf.gz.tbi `
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* ` spliceai_scores.masked.snv.hg19.vcf.gz `
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* ` spliceai_scores.masked.snv.hg19.vcf.gz.tbi `
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- * Including data (GRCh38) [ available here] ( https://download.molgeniscloud.org/downloads/vip/resources/GRCh38/ ) :
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+ * Including additional data (GRCh38) [ available here] ( https://download.molgeniscloud.org/downloads/vip/resources/GRCh38/ ) :
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* ` gnomad.genomes.v3.1.2.sites.stripped.vcf.gz `
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* ` gnomad.genomes.v3.1.2.sites.stripped.vcf.gz.csi `
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* ` hg38.phyloP100way.bw `
@@ -34,8 +40,6 @@ CAPICE can be used as online service at http://molgenis.org/capice
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* BCF tools v1.14-1
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* Python >=3.8
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- Note: Certain plugins might not be needed if training/predicting without using all possible features offered by CAPICE.
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-
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## Install
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The CAPICE software is also provided in this repository for running CAPICE in your own environment. The following
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sections will guide you through the steps needed for the variant annotation and the execution of making predictions
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