WARNING, skipping variant

[LIKUOKUO]

Hi Dr, Zeng，
I use an example vcf file to perform splicing prediction. However, it returns "WARNING, skipping variant: Variant not contained in a gene body. Do GTF/FASTA chromosome names match?" Could you please solve my issue?

pangolin examples/brca.vcf /data/reflib/gatk/hg19/Homo_sapiens_assembly19.fasta gencode.v38lift37.annotation.db brca_pangolin

[geertvandeweyer]

I think these warnings are benign and refer to variants that are just not locate in/near a gene according to the use gencode database. You can check the position in a genome browser to confirm.