Hello,
I am calling variants using HaplotypeCaller --> CombineGVCFs --> GenotypeGVCFs.
To determine the accessible genome, I emit all sites in the last step and I want to get several INFO annotations for all sites, such as DP, MQ, MQ0, .... Hence, I use VariantAnnotator with a regional all-individuals .bam file as input to get these annotations. However, this does not work as expected:
(1) Even after running this, the only annotations that non-variant sites get are: AN, DP. They do not get MQ, MQ0 etc. annotations. It should be possible to get these annotations for non-variant sites and I remember that it was possible with UnifiedGenotyper.
(2) Despite adding "--annotation RMSMappingQuality" and "--annotation MappingQualityZero", these annotations are not added, even not for variant sites.
Could you please let me know how to add annotations to non-variant sites using VariantAnnotator?
Here is my command line:
<br />
java-Xmx14000m \<br />
-jar GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar \<br />
-R reference.fa \<br />
-nt 8 \<br />
-T VariantAnnotator \<br />
--annotation RMSMappingQuality \<br />
--annotation Coverage \<br />
--annotation MappingQualityZero \<br />
--annotation AlleleBalance \<br />
--annotation SpanningDeletions \<br />
--annotation InbreedingCoeff \<br />
--annotation MappingQualityZero \<br />
-I all_individuals_region_X.bam \<br />
-V all_sites_region_X.vcf.gz \<br />
--out all_sites_region_X_annotated.vcf.gz \<br />
I tried both GATK 3.4-46 and 3.7.
Many thanks for your help.
Hannes