Using RDConnect_RNASeq for input to SmartRNASeqCaller

[brianjohnhaas]

Hi,

I used your nextflow workflow from here:
https://github.com/inab/RDConnect_RNASeq

to generate a gatk vcf file to be used as input to SmartRNASeqCaller.

The final output from running RDConnect_RNASeq is:
Step8_out.filtered.g.vcf

which contains PASS variants along with all those with filter fields set to non-pass values.

If I use this as input to SmartRNASeqCaller, it ends up selecting some non-pass variants as 'ok' variants.

Should we be running SmartRNASeqCaller on only the PASS variants from this vcf file?

thanks!

[brianjohnhaas]

I think I see the problem. The final output from running the genotyper isn't copied ('published' as per nextflow) into the specified output directory in the nextflow workflow.

[mbosio85]

Hi,

It look you already found that the answer to your question is that we used the 'PASS' variants as input for SmartRNASeqCaller.
Thanks for looking into the code and finding the issue in the RD_Connect_RNASeq pipeline :)
I'll update the code so that the correct file is in the output directory.

Cheers
Mattia

[brianjohnhaas]

Terrific. many thanks!

…

On Fri, Sep 6, 2019 at 9:30 AM Mattia Bosio ***@***.***> wrote: Hi, It look you already found that the answer to your question is that we used the 'PASS' variants as input for SmartRNASeqCaller. Thanks for looking into the code and finding the issue in the RD_Connect_RNASeq pipeline :) I'll update the code so that the correct file is in the output directory. Cheers Mattia — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4?email_source=notifications&email_token=ABZRKX6IQ7IQQCXT3BAQI5TQIJLQ5A5CNFSM4IUCQSUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6C3DGY#issuecomment-528855451>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZRKXYFEMCISGF5A3K23ODQIJLQ5ANCNFSM4IUCQSUA> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[PrincescaDorsaint]

Hi @mbosio85

Sorry for the late response. I just wanted to let you know that the adjustments you made on your pipeline now works with my VCF's.

Thanks!