strvctvre #1032
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strvctvre #1032
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bpblanken
commented
Feb 7, 2025
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| STRVCTVRE_REFERENCE_DATASETS_DIR=${STRVCTVRE_REFERENCE_DATASETS_DIR:-/var/seqr/strvctvre-reference-data} | ||
| STRVCTVRE_DOCKER_IMAGE="gcr.io/seqr-project/strvctvre-docker-image" | ||
| docker run --platform linux/amd64 -i -v $STRVCTVRE_DOCKER_IMAGE:$STRVCTVRE_DOCKER_IMAGE:ro $STRVCTVRE_DOCKER_IMAGE -p $WORKDIR "$@" |
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docker run -it --platform linux/amd64 -v /dev/shm:/dev/shm:rw gcr.io/seqr-project/strvctvre-docker-image -p /dev/shm/hg38.phyloP100way.bw -i /dev/shm/phase5.annotated.vcf.gz -o /dev/shm/out.vcf
this worked! Verified the StrVCTVRE annotation is present in the VCF in the right format.
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