Description
Verify
I have run VcfGrantham in the container lindenb/jvarkit:1b2aedf24 from DockerHub (https://registry.hub.docker.com/r/lindenb/jvarkit/tags), as well in a conda environment with the jvarkit mamba recipe (https://bioconda.github.io/recipes/jvarkit/README.html)
Subject of the issue
VcfGrantham is adding to my VCF header, but it is not annotating any missense variants that have been annotated using VEP
Example:
Header
##INFO=<ID=GRANTHAM_SCORE,Number=1,Type=Integer,Description="Max grantham score for this variant">
##vcfgrantham.meta=compilation:20230627132547 githash:1b2aedf24 htsjdk:3.0.4 date:20250104223445 cmd:--out /annotation_output/WI.20231213.hard-filter.isotype.biallelic_HDRsampleAnnotated.BLOSUM.VEP.GRANTHAM.vcf.gz /annotation_output/WI.20231213.hard-filter.isotype.biallelic_HDRsampleAnnotated.BLOSUM.VEP.vcf.gz
Missense Variant
I 4249 . G A 8681.29 PASS AC=6;AF=0.00490998;AN=1222;AS_BaseQRankSum=.;AS_FS=0;AS_InbreedingCoeff=0.4448;AS_MQ=59.92;AS_MQRankSum=.;AS_QD=31.8;AS_ReadPosRankSum=.;AS_SOR=0.945;DP=64566;ExcessHet=0;FS=0;InbreedingCoeff=0.4448;MLEAC=6;MLEAF=0.001838;MQ=59.92;NS=611;QD=31.8;SOR=0.945;VEP=A|missense_variant|MODERATE|WBGene00022277|WBGene00022277|Transcript|Y74C9A.3.1|protein_coding|5/5||||759|677|226|P/L|cCt/cTt|||-1||||c_elegans.PRJNA13758.WS283.csq_VEPsorted.gff3.gz|-3| GT:AD:DP:GQ:HDR:PL
The VCF I am working with contains ~3 million variants and 611 samples. I have tried on a subset of this VCF that contains 5,000 variants and 3 samples and I am getting the same results. No errors are returned.
Your environment
-
version of jvarkit
Name Version Build Channel
jvarkit 2024.08.25 hdfd78af_1 bioconda -
version of java
openjdk version "23.0.1-internal" 2024-10-15
OpenJDK Runtime Environment (build 23.0.1-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 23.0.1-internal-adhoc.conda.src, mixed mode, sharing) -
the value of
${JAVA_HOME}
/home/loconn13/mambaforge/envs/JVARKIT/lib/jvm -
which OS
Rocky Linux 8.8 (Green Obsidian)
Steps to reproduce
The script I have run in the container is:
$container_image="/pathToContainer/loconn13999-jvarkit_vcfgrantham_2025_01_04.sif" #(jvarkit:1b2aedf24)
$vcf="/pathToVCF/WI.20231213.hard-filter.isotype.biallelic_HDRsampleAnnotated.BLOSUM.VEP.vcf.gz"
$output_dir="/pathToOutputDirectory"
module load singularity
singularity exec --bind $output_dir:/annotation_output
$container_image
java -jar /opt/jvarkit/dist/jvarkit.jar vcfgrantham --out /annotation_output/$(basename $vcf .vcf.gz).GRANTHAM.vcf.gz /annotation_output/$vcf
Expected behaviour
VcfGrantham should add annotations to the INFO field of variants that have been annotated as "missense_variants"
Actual behaviour
VcfGrantham adds a header to the VCF but does not add annotations to the INFO field of missense variants