I use the Linux conda to install the GATK for uses and here's the conda list.
I use the code as this . I'm sure the path for these data is correct, but the Linux always return an error like ".fasta is not a recognized option" or like the figure i Shown here. SO , I am wondering what's wrong and how i can do to debug the code? Thx
/home/anaconda3/envs/velocyto/bin/gatk --java-options "-Xmx4g" HaplotypeCaller \
-R /media/workspace/refdata-cellranger-GRCh38-3.0.0/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta \
-I /media/workspace/A3_90/outs/possorted_genome_bam.bam \
-D /media/workspace/refdata-cellranger-GRCh38-3.0.0/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf \
-ERC GVCF \
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