AutoPVS1 use VEP to determine the effect of variants (SNVs, insertions, deletions, CNVs) on genes, transcripts, and protein sequence. To get HGVS name for the variant, indexed_vep_cache ...
Most of these can be installed via conda packages. Noting that some tools have different samtools version expectations, which can lead to problems. In particular the bioconda install of samtools is v0 ...
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