Entering edit mode
3.1 years ago
ommegang
▴
10
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?