AllelicCNV input files about detin HOT 4 CLOSED

Hey Erle,
Sorry to hear that.. I am not on the GATK team and often have trouble keeping track of where they're at in terms of development especially with the copy number tools. However, AllelicCNV doesn't seem to be deprecated:
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.6/org_broadinstitute_hellbender_tools_exome_AllelicCNV.php
Might I suggest running GATK using Docker? It might be easier than building the GATK yourself which I find often leads to problems.
https://hub.docker.com/r/broadinstitute/gatk/

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If you're looking for an alternative to GATK you could try facets. https://github.com/mskcc/facets. I would be happy to either add code or merge a pull request which supports the output of their model.

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Thanks! I got AllelicCNV to work in a Docker container, using these instructions (and increasing the memory allocated to Docker):
https://gatkforums.broadinstitute.org/gatk/discussion/10870/howto-run-gatk4-in-a-docker-container

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Hello,

If you're looking for an alternative to GATK you could try facets. https://github.com/mskcc/facets. I would be happy to either add code or merge a pull request which supports the output of their model.

Is this still a possibility to incorporate Facets? Given the GATK's "AllelicCNV" is indeed replaced by a tool that doesn't produce output required by "DE-tin" see here broadinstitute/gatk#6685
On the other hand, https://github.com/mskcc/facets seems quite straightforward.

P.S the link to GATK from DeTiN from Wiki doesn't seem to work anymore.

Thank you for your help in advance.
Best,
Nihir

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