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kipoi / kipoi-veff

Variant effect prediction plugin for Kipoi
https://kipoi.org/veff-docs
MIT License
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added --singularity to score_variants #26

Closed Avsecz closed 5 years ago

Avsecz commented 5 years ago

Example

Follow this tutorial: https://github.com/kipoi/examples/tree/master/2-score_variants and add --singularity to the command:

kipoi veff score_variants DeepBind/Homo_sapiens/TF/D00328.018_ChIP-seq_CTCF \
   --dataloader_args='{"fasta_file": "input/hg19.chr22.fa"}' \
   -i input/clinvar_20180429.pathogenic.chr22.vcf.gz \
   -s ref alt diff \
   -o /tmp/annotated.vcf --singularity