When combining Strelka and Mutect calls in SomaticCombineChannel, the way annotations are combined is inconsistent. For calls that are shared by both callers, DP comes from Strelka and AD comes from Mutect2. As a result, n_depth is usually different from the sum of n_ref_count and n_alt_count, even in the absence of a third allele. The same thing happens to t_depth, t_ref_count and t_alt_count, although t_depth is overwritten in the downstream process SomaticFacetsAnnotation with annotate-maf-wrapper.R from facets-suite.
The following snippet is supposed to annotate shared calls with Strelka annotations that Mutect does have, due to the pattern +FORMAT:
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bcftools annotate \ |
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--annotations ${isecDir}/0003.annot.vcf.gz \ |
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--columns +INFO,+FORMAT,Strelka2FILTER \ |
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--output-type z \ |
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--output ${isecDir}/0002.annot.vcf.gz \ |
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${isecDir}/0002.tmp.vcf.gz |
The plus sign means that the TAG is added if the source value is not missing and TAG is not present in the target file. Documentation can be found here. However, bcftools 1.9 in the current container doesn't actually behave this way. bcftools 1.11 does work the way we expect, and presumably newer versions do as well.
As for the over-writing behavior of facets-suite, either both values need to be overwritten, or neither of them. We do not want to change how facets-suite works, but the calculated depth does not necessarily have to be written into the maf.
When combining Strelka and Mutect calls in
SomaticCombineChannel, the way annotations are combined is inconsistent. For calls that are shared by both callers, DP comes from Strelka and AD comes from Mutect2. As a result,n_depthis usually different from the sum ofn_ref_countandn_alt_count, even in the absence of a third allele. The same thing happens tot_depth,t_ref_countandt_alt_count, althought_depthis overwritten in the downstream processSomaticFacetsAnnotationwithannotate-maf-wrapper.Rfrom facets-suite.The following snippet is supposed to annotate shared calls with Strelka annotations that Mutect does have, due to the pattern
+FORMAT:tempo/modules/process/SNV/SomaticCombineChannel.nf
Lines 92 to 97 in 8e4d68f
The plus sign means that the TAG is added if the source value is not missing and TAG is not present in the target file. Documentation can be found here. However, bcftools 1.9 in the current container doesn't actually behave this way. bcftools 1.11 does work the way we expect, and presumably newer versions do as well.
As for the over-writing behavior of facets-suite, either both values need to be overwritten, or neither of them. We do not want to change how facets-suite works, but the calculated depth does not necessarily have to be written into the maf.