I'm trying to annotate a VCF file (based on hg38) for consequences using bcftools csq. The VCF file looks finr to me, and I have verified that the assembly=38.
testfile="output/test.vcf" outfile="output/consequences/test-csq.csv" bcftools csq \ --local-csq \ --force \ --threads 120 \ --fasta-ref /SAN/reference_data/hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa \ --gff-annot /SAN/reference_data/ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.103.gff3.gz \ $testfile \ -Ot \ -o $outfile
The program runs without any error, and only prints a few warnings that it ignores *_random scaffolds and the like:
... ignored: KI270757.1 GRCh38 scaffold 1 71251 . . . ID=scaffold:KI270757.1;Alias=chrUn_KI270757v1,NT_187512.1 Indexed 185616 transcripts, 1281996 exons, 807371 CDSs, 336031 UTRs Ignored the following biotypes: 2x .. vault_RNA 2203x .. TEC 63894x .. lncRNA Calling...
I have verified that the proper chromosomes are not ignored. However, the file does not contain any consequence annotations:
# This file was produced by: bcftools +csq(1.12-1-g9aeb1aa+htslib-1.12-2-g385d248) # The command line was: bcftools +csq --local-csq --force --threads 120 --fasta-ref /SAN/reference_data/h # LOG Message # CSQ Sample Haplotype Chromosome Position Consequence
I'm clearly missing something here. Any idea what's going on?