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README.md

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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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* 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`
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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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## 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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