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Update annotations.md
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corrected nonfunctional links
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Marcel-Mueck authored Apr 4, 2024
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4 changes: 2 additions & 2 deletions docs/annotations.md
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Expand Up @@ -31,8 +31,8 @@ Download paths:
- [CADD](https://cadd.bihealth.org/download): "All possible SNVs of GRCh38/hg38" and "gnomad.genomes.r3.0.indel.tsv.gz" incl. their Tabix Indices
- [SpliceAI](https://basespace.illumina.com/s/otSPW8hnhaZR): "genome_scores_v1.3"/"spliceai_scores.raw.snv.hg38.vcf.gz" and "spliceai_scores.raw.indel.hg38.vcf.gz"
- [PrimateAI](https://basespace.illumina.com/s/yYGFdGih1rXL) PrimateAI supplementary data/"PrimateAI_scores_v0.2_GRCh38_sorted.tsv.bgz"
- [AlphaMissense](https://storage.googleapis.com/dm_alphamissense/AlphaMissense_hg38.tsv.g)
Also a reference GTF file containing transcript annotaions should be provided, this can be downloaded from [here](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v44.annotation.gtf.gz)
- [AlphaMissense](https://storage.googleapis.com/dm_alphamissense/AlphaMissense_hg38.tsv.gz)
Also a reference GTF file containing transcript annotaions should be provided, this can be downloaded from [here](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.annotation.gtf.gz)


## Configure the annotation pipeline
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