Error for exon data

[gongxuesusan]

Dear There,

I tried to use bcbio_nextgen.py to detect mutation by four callers (mutect, varscan, freebayes, vardict) for exon sequencing data. But I ran into the below error.

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb):

ERROR The invalid arguments or inputs must be corrected before the GATK can proceed

ERROR Please do not post this error to the GATK forum

ERROR

ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Argument with name 'allow_potentially_misencoded_quality_scores' isn't defined.

ERROR ------------------------------------------------------------------------------------------

' returned non-zero exit status 1

Does anyone how to fix it? Thank you very much.

Xue

[chapmanb]

Xue; Sorry about the issue. It looks like you have an older version of GATK (2.2) installed which does not support some of the options used in bcbio. If you want to use GATK for annotations of variant calls you can install the latest via the instructions here:

https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#gatk-and-mutect

Alternatively if you want to skip GATK, you can remove the 2.2 jar line (gatk -> dir) from your installed /path/to/bcbio/galaxy/bcbio_system.yaml file. Older versions of bcbio, if you've installed a while ago, used to install 2.2 but we now skip installing GATK completely unless you want to install it manually.

Hope this helps.

[lpantano]

Closing this since it seems it worked at the end. Let us know if there is any other issue.

thanks!