bcftools csq creates no output

Question

[ommegang]

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   [2]Message
# CSQ   [2]Sample       [3]Haplotype    [4]Chromosome   [5]Position     [6]Consequence

I'm clearly missing something here. Any idea what's going on?

Answer 1

[ommegang]

The problem was that the gff file named chromosomes as 1, 2, 3, the other files as chr1, chr2, etc. :-/