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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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CancerCaller: normal sample is not a valid sample. #164

Closed gamzemdn closed 3 years ago

gamzemdn commented 3 years ago

Hi! I am providing the same normal-tumor pair with Mutect2 but I got the error in title. My code is below octopus \ -R '/home/gamze/Desktop/BIO_proje1/Homo_sapiens_UCSC_hg38/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa' \ -I '/home/gamze/Desktop/BIO_proje1/TUMOR1_BWA_MUTECT/germrecalibratedoutput.bam' \ '/home/gamze/Desktop/BIO_proje1/TUMOR1_BWA_MUTECT/tumor1recalibratedoutput.bam' \ --normal-sample germrecalibratedoutput \ --forest '/home/gamze/Downloads/octopus_forests_germline.v0.7.2.forest.gz' \ --somatic-forest '/home/gamze/Downloads/octopus_forests_somatic.v0.7.2.forest.gz' \ -o tumor.vcf.gz

germrecalibratedoutput is my normal file. Can somebody point me to the right direction?

Thanks