Commit f2aea99b authored by Severine Duvaud's avatar Severine Duvaud
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Removed unused directory

parent 74bf18b6
//
Updated by dteixeir on 15/02/16
Created by sduvaud on 10/02/16.
extends layout
block content
div.container
div(class="jumbotron")
h1 Documentation
p Specifications and open questions.
p Back to #[a(href="/") Home Page. #[span]]
h4 Current implementation
img(src="/img/current_implementation.jpg" class="img-thumbnail img-responsive")
h5 Comments
p
ul
li reference genome: In #[a(target="_blank" href="https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit") Beacon 0.2 specifications], the values expected for human data is of GRCh? format, whereas arrayMap uses hg?? nomenclature.
li allele: In #[a(target="_blank" href="https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit") Beacon 0.2 specifications], the parameter is required. However, it does not make sense at all for arrayMap (in which no sequence related data exists).
li variantClass: This is a new parameter. The value equals DUP corresponds to SEGTYPE=1 (gain) in arrayMap, while DEL is for SEGTYPE=-1 (loss). The parameter is mandatory.
li sampleuid: This is DEBUG info.
li matchedSegment: This is DEBUG info.
br
h5 Example
p Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: #[a(target="_blank" href="/v0.2/query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL") query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL]
br
h5 Outcome from the meeting with Jordi (Feb, 10, 2016):
p It chould be ok to have the variantClass in Beacon v0.3. As for ranges, this is more complicated and requires lots of discussions. We will probably go in 2 steps:
ul
li add P (duPlication) to the list of allowed values for the allele parameter.
li modify I (insertion) slightly by making the "sequence" string optional, i.e. be fuzzy about what was inserted.
p and then
ul
li proper variantClass
li ranges (defined as start/stop position, e.g. [200000,30000] #[span(style="font-weight: bold;") or] start and length, e.g. 20000:100000)
h4 API description
br
h5 QueryResource
table(class="table table-responsive table-striped")
tr
th(style='width: 25%') Parameter name
th(style='width: 25%') Required in Beacon
th(style='width: 25%') Required in Beacon-arrayMap
th(style='width: 25%') Comment
tr
td chromosome
td yes
td yes
td no control for now (dropdown list?)
tr(class="text-danger")
td position
td yes
td yes
td no control for now (>0)
tr
td reference
td yes
td no
td Genome ID. Should be added
tr(class="text-danger")
td allele
td yes
td no
td Not applicable to arrayMap (no sequence info).
tr
td dataset_id
td no
td yes
td ICDM
h5 ResponseResource
table(class="table table-responsive table-striped")
tr
th(style='width: 25%') Parameter name
th(style='width: 25%') Required in Beacon
th(style='width: 25%') Required in Beacon-arrayMap
th(style='width: 25%') Comment
tr
td exists
td yes
td yes
td value=overlap
tr
td alleles
td no
td no
td
tr
td observed
td no
td no
td
tr
td info
td no
td yes
td value=ok
tr
td error
td no
td yes
td value=null
h4 Forthcoming implementation: Open questions
br
h5 Imprecise structural variants:
div
p Exact positions are definitely not suitable for arrayMap. We should be able to request for ranges rather than positions. However, the issue with using ranges is that the start and end positions are imprecise in arrayMap.
div(class="alert alert-info") In the VCF, there is a field for the symbolic alternate alleles for imprecise structural variants in the meta-information lines.<br>See #[a(target="_blank" href="https://samtools.github.io/hts-specs/VCFv4.2.pdf") the VCF 4.2 specifications] for more details.
p Example:
table(class="table")
tr
th CHROM
th POS
th ID
th REF
th ALT
th QUAL
th FILTER
th INFO
th FORMAT
th NA00001
tr
td 1
td 2827694
td rs2376870
td CGTGGATGCGGGGAC
td C
td .
td PASS
td SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68
td GT:GQ
td 1/1:13.9
tr
td 1
td 12665100
td .
td A
td <DUP>
td 14
td PASS
td SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500
td GT:GQ:CN:CNQ
td ./.:0:3:16.2
p Description of the INFO field:
ul
li SVTYPE=(DEL|DUP|INS|CNV) - mandatory: Type of structural variant.
li END=integer - mandatory: End position of the variant
li SVLEN=integer - Diff in length btw Ref and Alt. Negative in case of deletion.
li CIPOS=integer - Confidence interval around position (POS).
li CIEND=integer - Confidence interval around end position (END).
br
h5 Use-cases:
div
p Now, how should we proceed with the ranges in the following cases?
div(class="row")
div(class="col-md-3")
img(src="/img/chromosome15.png" class="img-thumbnail img-responsive")
em Only either start or stop postion are in the CNV region, i.e. the queries range is not fully covered.
div(class="col-md-3")
img(src="/img/chromosome20.png" class="img-thumbnail img-responsive")
em The range is embedded within a CNV region.
div(class="col-md-3")
img(src="/img/chromosome13.png" class="img-thumbnail img-responsive")
em The range matches 2 CNV regions.
div(class="col-md-3")
img(src="/img/chromosome11.png" class="img-thumbnail img-responsive")
em The 2 range overlaps many CNV regions.
h5 SEGVALUE
p What is the meaning of SEGVALUE? Can/should we use it as a filter (such as a FDR)?
h4 Info endpoint:
p Link #[a(target="_blank" href="/info") here].
div
img(src="/img/info_structure.png" class="img-thumbnail img-responsive")
br
em (Truncated version.)
br
p Open questions:
ul
li In #[a(target="_blank" href="https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit") Beacon 0.2 specifications], 'variants' is a mandatory property of #[span(style="font-weight: bold;") DataSizeResource] and its value was arbitrary set to -1. Now, we have to decide whether we should:
ol
li stick to -1.
li use the property 'variants' to count the number of segments (for instance).
li ask the Beacon team if we can make this optional property.
li ask the Beacon team if we can change the property name.
li In #[a(target="_blank" href="https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit") Beacon 0.2 specifications], 'reference' is a mandatory property of #[span(style="font-weight: bold;") DataSetResource]. The problem is that, in arrayMap, the genome version is linked to a given sample, and not to a cancer tissue type. Moreover, there can be more than one genome version in a sample. Now, we have to decide whether we should:
ol
li assign it a fake default value.
li assign it the first reference genome's value of the data structure.
li ask the Beacon team if they can make this optional property.
li ask the Beacon team if they can replace the property type by a list of strings (instead of a string).
li clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)
div(class="alert alert-info") The Beacon 0.3 specifications don't include any of the above proposals.
extends layout
block content
h1= message
h2= error.status
pre #{error.stack}
extends layout
block content
h1 arrayMap data accessed using node express (experimental)
p The are samples here
a(href='/samples?limit=10') Samples (first 10)
p
a(href='/samples') Samples (all)
p
a(href='/v0.2/query?chromosome=9&position=57649422') Implementation of Beacon v0.2 draft
p
a(href='/v0.2/query?chromosome=9&position=57649422&dataset=8010/3') Implementation of Beacon v0.2 draft with dataset
p
a(href='/info') Drafts info
doctype html
html
head
title= title
link(rel='stylesheet', href='https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css')
link(rel='stylesheet', href='https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css')
body
block content
extends layout
block content
h1.
Samples
ul
each sample, i in samples
li= sample.CITY
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