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Annotation is lost when merging GVCF files with GenotypeGVCFs
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.