CHM13.GFF3.V4 annotations cause the phase error in bcftools
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Hello,
I have issues with gff annotation using bcftools. At first, I used the following command
bcftools csq -f chm13_grch38_Y_added.fa -g chm13.draft_v1.1.gene_annotation.v4.gff3 ../longread/samtools/T15/T15_chm13_sorted.vcf -O z -o T15_chm13_sorted_annotated.vcf
then got the error message saying Could not parse the line, "Parent=transcript:" not present so I adjusted gff file using zcat chm13.draft_v1.1.gene_annotation.v4.gff3.gz \ | gawk 'BEGIN{IGNORECASE=0} $0 ~/^#/ || ($3 != "gene" && $3 != "transcript" ) { $0=gensub(/Parent=(.+?_T[^;]+)/, "Parent=transcript:\\1", "g", $0); print; next} $0 !~/^#/ { gsub(/ID=/, "ID="$3":"); $0=gensub(/Parent=(.+?_G[^;]+)/, "Parent=gene:\\1", "g", $0); print }' \ | bgzip -c > chm13.draft_v1.1.gene_annotation.v4.fix.gff3.gz to fix the error message.
But then I still get the phase error message
Error: GFF3 assumption failed for transcript CHM13_T0000003, CDS=111940: phase!=len%3 (phase=2, len=379)
and got the following message after --force running it.
Warning: GFF3 assumption failed for transcript CHM13_T0110841, CDS=23883573: phase!=len%3 (phase=0, len=607)
If bcftools seems to cause phase errors which tool do you recommend to use to annotate variant calls on CHM13?
Seems like others are experiencing the same issue here
Cheers,
DK