Kathrin B
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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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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/...