Depth of informative coverage for each sample (DP)
Category Variant Annotations
OverviewDepth of informative coverage for each sample.
This annotation is similar to the sample-level DP annotation, which counts read depth after general filtering, but with an extra layer of stringency. Its purpose is to provide the count of reads that are actually considered informative by HaplotypeCaller (HC), using pre-read likelihoods that are produced internally by HC.
In this context, an informative read is defined as one that allows the allele it carries to be easily distinguished. In contrast, a read might be considered uninformative if, for example, it only partially overlaps a short tandem repeat and it is not clear whether the read contains the reference allele or an extra repeat.
See the method documentation on using coverage information for important interpretation details.
- This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator).
- DepthPerAlleleBySample calculates depth of coverage for each allele per sample (AD).
- Coverage gives the filtered depth of coverage for each sample and the unfiltered depth across all samples.
GATK version 22.214.171.124 built at Thu, 5 Dec 2019 09:51:56 -0500.
Hello! I encountered thousands of the following warnings when calling gvcf using GATK 4.2. (Only appeared on part of my samples).
DepthPerSampleHC - Annotation will not be calculated at position ________ and possible subsequent; genotype for sample _______ is not called.
StrandBiaBySample - Annotation will not be calculated at position ________ and possible subsequent; genotype for sample _______ is not called.
Does this warning mean that the generated gvcf is not good? Or I can just ignore those warnings?
Please sign in to leave a comment.