Julien Soubrier
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Activity overview
Latest activity by Julien Soubrier-
Julien Soubrier commented,
Thanks Genevieve-Brandt-she-her, adding the contig dictionary to the GENOTYPES input VCF (e.g., using UpdateVCFSequenceDictionary) solved the issue with the latest gatk version (4.1.8.1).Details i...
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Julien Soubrier commented,
Hi Genevieve-Brandt-she-her, sure, sorry about that: > gatk CheckFingerprint -I analysis_ready_bam/sample.bam --GENOTYPES tmp_picard_CheckFingerprint/sample_SID_Agena.vcf --HAPLOTYPE_MAP /ngs_pipel...
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Julien Soubrier created a post,
Trouble running CheckFingerprint with gatk-4.1.8.1
Hi GATK team/community, I don't seem to be able to get CheckFingerprint to run with either gatk-4.1.4.1 or gatk-4.1.8.1, while it's working fine with gatk-4.1.2.0 and gatk-4.1.3.0. What I tried so ...
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Julien Soubrier commented,
Hi all, Trying the new release overnight, I re-ran the exact same command on the same data set and it completed with no error for the 11 exomes. Thanks a lot David Benjamin, Bhanu Gandham and the r...
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Julien Soubrier commented,
David Benjamin, I see you are currently working on https://github.com/broadinstitute/gatk/pull/6498. Would you still need examples of this happening? Happy to try to upload everything as a 'bud rep...