using loftee and GRCh38 about loftee

[matthdsm]

Hi,

I'd like to follow up on this question, is there a liftovered version of the human ancestor file available? Or can we just use the same fasta file?

Thanks
M

[snashraf]

Hi can you please share whatever command you have been using for Loftee annotation ? I am using below command and not getting even one LOF Mutation in my VCF files.

perl /gpfs/software/genomics/VEP/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl -i PMC01_jointCalling.filtered.snps.indels.vcf --cache --assembly GRCh37 --offline --dir_cache /gpfs/projects/vep/ --vcf --everything --sift --polyphen --hgvs --fasta /gpfs/projects/refData/Homo_sapiens.GRCh37.dna.primary_assembly.fa --force --symbol --dir_plugins /gpfs/software/genomics/VEP/loftee -o PMC01_jointCalling.filtered.snps.indels_VEP.vcf
perl /gpfs/software/genomics/VEP/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl -i PMC01_jointCalling.filtered.snps.indels.vcf --cache --assembly GRCh37 --offline --dir_cache /gpfs/projects/vep/ --vcf --everything --sift --polyphen --hgvs --fasta /gpfs/projects/refData/Homo_sapiens.GRCh37.dna.primary_assembly.fa --force --symbol --dir_plugins /gpfs/software/genomics/VEP/loftee ----plugin LoF -o PMC01_jointCalling.filtered.snps.indels_VEP.vcf

[rvernica]

@matthdsm did you find a resolution to this issue?

[matthdsm]

Hi @rvernica

Not exactly, I've just started using the reference genome.
Cheers
M