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mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
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--genome error when using mutiple vcf files #2

Closed deb0612 closed 3 years ago

deb0612 commented 3 years ago

Dear sir, I had try to use the command: bash AutoMap_v1.0.sh --vcf 0366.HC.vcf 0367.HC.vcf 0368.HC.vcf /0369.HC.vcf --out /working_space/ --genome hg38 and got the message below:

bcftools higher or equal to v1.9 bedtools higher or equal to v2.24.0 perl higher or equal to v5.22.0 R higher or equal to v3.2.0 Parameters used by default: ERROR: You need to provide the genome version through --genome option (hg19 or hg38). Exit.

I sure I had provided the "--genome" option.

mquinodo commented 3 years ago

Dear user, for the --vcf option, you need to separate the files with commas. Therefore, the correct command would be: bash AutoMap_v1.0.sh --vcf 0366.HC.vcf,0367.HC.vcf,0368.HC.vcf,0369.HC.vcf --out /working_space/name --genome hg38