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Clarify the counts in Beacon response

Open juhtornr opened this issue 7 years ago • 7 comments

Clarify what different counts actually mean in Beacon response.

Related to #105

juhtornr avatar Nov 19 '18 15:11 juhtornr

Here is our interpretation of what these counts mean.

Context (model) Key (field) Description in specification What we think it means
BeaconDataset variantCount Total number of variants in the dataset Total number of variants in the dataset, e.g. total number of rows in the database/VCF where referenceBases can appear multiple times (in the same position), e.g. T > C and T > A would be two variants
BeaconDataset callCount Total number of calls in the dataset Number of calls made to variants in the dataset, possibly returning more results (variants) than the number of calls. So variantCount > callCount. e.g., referenceBases are unique/distinct and can appear once only (in the same position), e.g. T > C and T > A would be one call (that resulted in two variants)
BeaconDataset sampleCount Total number of samples in the dataset Number of test subjects (people) in the dataset
BeaconDatasetAlleleResponse variantCount Number of variants matching the allele request in the dataset Number of exact matches, so in case of a hit when searching without wildcards, this is always 1, e.g. look for T > C and find match with T > C. With wildcards variantCount can be more than 1, e.g T > N could match T > A and T > C making variantCount 2. Essentially number of "rows" that were matched from database. When no results are found, this is 0
BeaconDatasetAlleleResponse callCount Number of calls matching the allele request in the dataset We don't know what this means
BeaconDatasetAlleleResponse sampleCount Number of samples matching the allele request in the dataset Equal to "AC" "Allele Count", number of test subjects (people) that have this variant, e.g. 100 people of 1000 tested people have this variant, makes allele count (sample count in context of allele response) 100 and frequency 0.1

We would like to know how to interpret these counts and validate our interpretation. Adding an example dataset (VCF) to the specification, and how to compute the counts on that dataset, would clarify this.

teemukataja avatar Nov 26 '18 07:11 teemukataja

This is great! We'll (all) should comb through & then move tis, also, to the Beacon website.

To be clarified e.g.:

  • "Total number of samples in the dataset" ... is a clear reason why we need an assumed data model. A typical cancer dataset could have several callsets for each of several biosamples from each of different individuals.
  • Predicting variable base numbers; e.g. when adding a phenotype query, providing the number of matching biosamples as basis for e.g. variant frequency calculations. This doesn't have to be in the documentation right now (we have only "Bio0ontology" queries in our demonstrator, but not yet in the code here); but we should use compatible semantics.

mbaudis avatar Nov 26 '18 12:11 mbaudis

@teemukataja The statement

sampleCount	Total number of samples in the dataset	Number of test subjects (people) in the dataset

is misleading. A dataset in the "variant dataset" sense is a combination of 1 -> n "callsets", i.e. outputs from experiments on the material of a biosample. So the correct term here would be callsets (as said above, even "biosamples" would be tricky, since several replicates could have been included...) Individuals is definitely wrong. "samples" kind of skirts the problem, since the word is weakly defined; but assuming a VCF-like structure, the "sample"s would correspond to "callset"s (at least in standard use).

mbaudis avatar Nov 26 '18 12:11 mbaudis

Hi guys! I don't think sampleCount (in BeaconDatasetAlleleResponse) is the same as AC field in VCF.

Look at this example extracted from the 1000 genoms project:

21      9489357 rs566796439;rs544784469 CATAT   CAT,C   100     PASS    AC=5,11;AF=0.000998403,0.00219649;AN=5008;NS=2504;DP=14652;EAS_AF=0.001,0;AMR_AF=0,0;AFR_AF=0.003,0.0076;EUR_AF=0,0.001;SAS_AF=0,0;VT=INDEL;MULTI_ALLELIC       GT
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We have 2504 samples (NS) and AC=5,11 (there are 2 alternates). The VCF spec says:

AC: allele count in genotypes, for each ALT allele, in the same order as listed

This means you count the number of 1s in the genotypes (e.g. 0/1) (if there is more than one alternate, it would be represented as 0/2 or 3/0, etc.). So, for the first alternate AC=5 (there are two 1| and three |1) and for the second alternate AC=11 (there are five |2 and six 2| ).

I remember discussing what was the matching between the Beacon fields and the VCF fields, and somebody said (I couldn't find the conversation): frequency = AF, variantCount=AC, callCount=AN and sampleCount=NS but this may be true for AF and AC but not for AN and NS.

These are their definitions:

AF: allele frequency for each ALT allele in the same order as listed

You can calculate it: for the first alternate, AF=0.000998403=5/5008 (=AC/AN). For the second alternate, AF=0.00219649=11/5008

AN: total number of alleles in called genotypes

Reading the documentation and checking real VCFs, you can deduce that AN > NS and usually AN=2*NS but you can also calculate it: it's the number of elements in the genotype (e.g. if we only have 3 samples and the genotypes are 0|0 .|. 1|0, AN would be 4 because we don't have information for the 2nd sample).

NS: Number of samples with data

So, NS definition cannot be used because in the Beacon we need the number of samples with the matching allele (that is, samples which have something different than 0 in the genotype, e.g. 1|0 or 0|1, in our example we have 5 samples which show the first alternate and 11 samples which show the second alternate)

I think the main clarification is what callCount means in BeaconDatasetAlleleResponse as it does not match with the VCF definition of AN and nobody seems to know what it really means... Probably, after clarifying this, we will then know what it means in the context of the BeaconDataset (not sure it's what you wrote in the first comment).

Also, I think that sampleCount does not mean the number of individuals as you can have multiple samples of the same person (and then I think the definition would be "Total number of individuals in the dataset", but maybe this is what we really meant and we just need to fix the definition).

sdelatorrep avatar Dec 04 '18 14:12 sdelatorrep

(edited) @sdelatorrep we found some cases that are an exception to the AN > NS e.g. for Y chromosome AN = NS (might be the only chromosome)

Y	2664779	.	TTGA	T	100	PASS	AA=TTGA;AC=3;AN=1233;DP=4783;NS=1233;VT=INDEL;AMR_AF=0.0000;AF=0.0024;AFR_AF=0.0000;EUR_AF=0.0000;SAS_AF=0.0115;EAS_AF=0.0000	GT

what do we do in those cases ? - also the case where there is no AN - MT chromosome is one of those cases should, we just assume AN =2*NS ?

Most of these (edge) cases relate to the VCF format quirks rather than the beacon specification.

I think we need to handle frequency calculation clarification in a different issue, as we assumed that AAF might make more sense instead of the AF, but then again it is not clear from the text in the specification, what this means:

Frequency of this allele ....

also, thanks for the pointers and clarifications :) - much appreciated.

blankdots avatar Dec 05 '18 14:12 blankdots

Jordi and I have been discussing this. We think that some of the field names in BeaconAlleleResponse should make explicit that they match the request (e.g. variantCount vs variantMatchingCount and sampleCount vs sampleMatchCount) but, as this is a big change, this can be postponed for a later release. However, we think we need a new field named sampleTotalCount in the response because sampleCount will be the samples with the requested allele and having the total count of samples is useful for the user querying the beacon (otherwise, they need to do a new request to get the sampleCountin BeaconDataset). This is also useful if the query returns multiple matches which should be aggregated.

We also think that the most useful meaning of callCount would be the same as AN in the VCF spec (total number of alleles in called genotypes), it gives more information about the response and it can be used to calculate the frequency (see my comment above to see how AN is calculated). The definition in the Beacon spec should be adapted to this but I don't think I'm the best person to do so... probably @mbaudis ;)

sdelatorrep avatar Dec 17 '18 13:12 sdelatorrep

I've created a PR #258 with the clarification and a Wiki page explaining how to calculate these counts with an example (the same I provided here).

sdelatorrep avatar Jan 17 '19 14:01 sdelatorrep