Hello,
I use GATK version 4.1 to annotate a vcf with the following command :
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx5g -jar gatk-package-4.1.1.0-local.jar VariantAnnotator -R /sandbox/resources/species/human/ensembl/release-75/Homo_sapiens.GRCh37.75.dna.toplevel.fa -V GQPDOMB-stats.vcf -O rsID_GQPDOMB.vcf --dbsnp
/sandbox/resources/species/human/ensembl/release-75/dbSNP_b150_GRCh37_00-All.vcf.gz
However, it only looks for rs IDs for the first 5. How is it possible to solve this problem so that it can find the rs IDs of the entire file?
Thanking you for your help
I use GATK version 4.1 to annotate a vcf with the following command :
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx5g -jar gatk-package-4.1.1.0-local.jar VariantAnnotator -R /sandbox/resources/species/human/ensembl/release-75/Homo_sapiens.GRCh37.75.dna.toplevel.fa -V GQPDOMB-stats.vcf -O rsID_GQPDOMB.vcf --dbsnp
/sandbox/resources/species/human/ensembl/release-75/dbSNP_b150_GRCh37_00-All.vcf.gz
However, it only looks for rs IDs for the first 5. How is it possible to solve this problem so that it can find the rs IDs of the entire file?
Thanking you for your help