Error in VCF format? - Githubissues

10XGenomics / vartrix

Single-Cell Genotyping Tool

MIT License

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Error in VCF format? #46

Open xiweiwu opened 4 years ago

xiweiwu commented 4 years ago

I have generated VCF file using VarScan2. However, it seems that VarTrix does not detect any variants in the vcf file. Is there an example VCF file that I can look at to make sure my VCF format is correct?

[E::vcf_hdr_read] No sample line 22:19:44 [ERROR] Warning! Zero variants found in input VCF. Output matrices will be by definition empty but will still be generated. 22:19:44 [ERROR] The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs?

pmarks commented 3 years ago

@xiweiwu my apologies for the delay. Are you still having this issue? If so, please post some example entries from the VCF you are using. Thanks!.