which version of GATK should i use?

getzlab / deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

BSD 3-Clause "New" or "Revised" License

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which version of GATK should i use? #12

Closed haoziyeung closed 6 years ago

haoziyeung commented 6 years ago

Hello,i'm using gatk4,and i can't find AllelicCNV

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gpfs/users/yanghao/software/anaconda2/share/gatk4-4.0.3.0-0/gatk-package-4.0.3.0-local.jar AllelicCNV

A USER ERROR has occurred: 'AllelicCNV' is not a valid command.

can you tell me which version should i use? many thanks.

@amarotaylor

amarotaylor commented 6 years ago

I'm guessing you found this.. but linking here for others. Did not see this issue earlier sorry about that. https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.6/org_broadinstitute_hellbender_tools_exome_AllelicCNV.php

haoziyeung commented 6 years ago

Many thanks.