error to import vcf - Githubissues

abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

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error to import vcf #242

Open deb0612 opened 3 years ago

deb0612 commented 3 years ago

Dear sir, When I use cnvnator -root.root -vcf file.vcf. It shows error below: Parsing file file.vcf ... [E::hts_open_format] Failed to open file "file.vcf" : No such file or directory Vcf parser: Can't open file 'file.vcf'. Vcf parser: finished after reading 0 records. Total of 0 SNPs were placed.

arpanda commented 3 years ago

Hi, I am not sure about the content of the vcf file. Probably, the vcf file has some issue. To check the file has any issue or not, can you please try to use bcftools/samtools to view the content.

Also, I would recommend to use the updated version of cnvnator called CNVpytor (https://github.com/abyzovlab/CNVpytor).