Kathrin B
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Activity overview
Latest activity by Kathrin B-
Kathrin B created a post,
FastaAlternateReferenceMaker generates same sequence for multisample vcf
REQUIRED for all errors and issues: a) GATK version used: v4.2.5.0b) Exact command used: I used SelectVariants to generate one vcf file per sample and then used: FastaAlternateReferenceMaker -R g...
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Kathrin B commented,
Hi Genevieve Brandt (she/her), Thank you so much for your help with this. Everything was messed up after installing the conda environment, but I finally got it to work again, and I'll just proceed ...
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Kathrin B commented,
Genevieve Brandt (she/her), I switched to bioconda, but I'm still struggling with the environment. Do I have to create one myself?
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Kathrin B commented,
Hi Genevieve, sorry for the late reply! No, I'm not using Docker as I'm connecting to a HPCC where I don't have admin privileges. I followed the article here to set up the environment.
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Kathrin B created a post,
CNNScoreVariants Issues with environment and Java version
AnsweredREQUIRED for all errors and issues: a) GATK version used: 4.2.5.0b) Exact command used: gatk CNNScoreVariants I "/path/to/directory/sample.bam" -V "/path/to/directory/sample.g.vcf.gz" -R "/path/to/...