VariantAnnotator produces values different from those of HaplotypeCaller
Hi! I wanted to annotate VCF files produced by other variant callers with BaseQRankSum, ReadPosRankSum, StrandOddsRatio metrics using VariantAnnotator. I tested VariantAnnotator on VCF file produced by HaplotypeCaller to check if VariantAnnotator will yield the same values for the metrics as HaplotypeCaller. I ran VariantAnnotator with the same read filters as HaplotypeCaller uses. VariantAnnotator produced different values for some variants. For BaseQRankSum metric it produced different values for 8 variants out of total 145, for ReadPosRankSum - the same 8/145, for StrandOddsRatio - 144/145.
Why does VariantAnnotator produce values different from those produced by HaplotypeCaller? Is it because VariantAnnotator does not use pre-read likelihoods to compute metrics' values like HaplotypeCaller does as mentioned in article about AlleleFraction annotation? Is there any way to make VariantAnnotator produce the same values as HaplotypeCaller?
GATK version used:
4.6.1.0
Exact command used:
gatk VariantAnnotator \
--disable-read-filter PrimaryLineReadFilter \
--read-filter PassesVendorQualityCheckReadFilter \
--read-filter MappedReadFilter \
--read-filter NotDuplicateReadFilter \
--read-filter WellformedReadFilter \
--read-filter NotSecondaryAlignmentReadFilter \
--read-filter GoodCigarReadFilter \
--read-filter NonZeroReferenceLengthAlignmentReadFilter \
--read-filter MappingQualityAvailableReadFilter \
--read-filter MappingQualityReadFilter \
--annotation BaseQualityRankSumTest \
--annotation StrandOddsRatio \
--annotation ReadPosRankSumTest \
--reference ${reference_filepath} \
--input ${bam_filepath} \
--variant ${vcf_filepath} \
--output ${annotated_vcf_filepath}
-
VariantAnnotator does not use similar ways to analyze variant sites as HaplotypeCaller so numeric values could be different between 2 tools. VariantAnnotator uses direct reads to collect metrics however HaplotypeCaller has local assembly and realignment.
Regards.
-
Thanks!
Please sign in to leave a comment.
2 comments