Warning: fewer CSQ fields than expected

[kuaileshizuihao]

After merging files from different samples using "bcftools merge", I encountered a problem while using bcftools +split-vep, which resulted in this error. I filtered out the lines causing the error and saved them as Error.vcf. Initially, I suspected that the “|” symbol in the GT field might be interfering with the recognition of the fields, so I replaced all GT information with “.” However, the error still persists. This has been a source of frustration for me for two weeks. Thank you very much for your assistance!

bcftools +split-vep "/ehpcdata/analysis/chenhaijie/Compare/Error.vcf" -H -d -A tab -f '%ID\t%CHROM\t%REF\t%ALT\t%CSQ' -s all:missense+ -o /ehpcdata/analysis/chenhaijie/Compare/ErrorSplited.vcf
# Warning: fewer CSQ fields than expected at chr1:201359246, filling with dots. This warning is printed only once.

Error.vcf.zip