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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Trio pipeline #2961

Closed kokyriakidis closed 5 years ago

kokyriakidis commented 5 years ago

@chapmanb

1) I would like to run a trio analysis in whole exome samples. Can I use all callers (strelka2, deepvariant. vardict, gatk etc) for a trio analysis with samples having the same batch name? Can I use the ensemble method?

2) I am also trying to do CNV analysis in this trio. Can I add all svcallers? Do all work with single germline sample?

It would also be nice to specify in the documentation:

Which callers can be used for Germline Variant Calling Which callers can only be used for Somatic (Tumor-Normal) Variant Calling Which callers can be used for Germline SV Calling Which callers can only be used for Somatic (Tumor-Normal) SV Calling Which callers can be user for Trio analysis

roryk commented 5 years ago

Thanks, I think we shouldn't be adding that column unless it is there, so it is a bug.

kokyriakidis commented 5 years ago

Running the command again caused the same error when changed PED. Should I delete the work folder and run it again?

roryk commented 5 years ago

Heya, it will still be using the broken PED file if it is on the disk, I think if you just delete the PED file in the GEMINI directory it will populate a new one.

roryk commented 5 years ago

I'll update the documentation to mention we require the ethnicity as well, sorry about that.

kokyriakidis commented 5 years ago

It finally run successfully! Thanks a lot all of you for the help!

roryk commented 5 years ago

Great! Sorry for the problems!