Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Annotation is lost when merging GVCF files with GenotypeGVCFs

sheilaztsheilazt ValenciaMember

Dear GATK team,
The StrandBiasBySample annotation works fine with the HaplotypeCaller but then when I merge all my GVCF files into one with the GenotypeGVCFs tool I loose this information for all my variants. Here is the command I use.
java -jar /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/mapping/GenomeAnalysisTK.jar --analysis_type GenotypeGVCFs -R /data/references/human/genome/GRCh38_hg20/GRCh38.fasta --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/A1048_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/A333_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/A798_REP_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/A846_URG_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/A899_URG_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P283_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P284_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P285_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P288_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P289_INH_raw.g.vcf.gz --variant /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/P291_INH_raw.g.vcf.gz -o /data/results/Bioinfo/BF18_TargetSeq_Genomica/results/variant_calling/all_samples.vcf --includeNonVariantSites

Is there any way to safely join my GVCF files into one and keep the StrandBiasBySample annotation for my variants?

Thanks very much in advance.

Regards,

Sheila

Comments

Sign In or Register to comment.