[Bioc-devel] zero-width ranges representing insertions
Hervé Pagès
hpages at fredhutch.org
Tue Mar 17 11:41:37 CET 2015
On 03/16/2015 07:36 PM, Valerie Obenchain wrote:
> On 03/16/2015 05:31 PM, Hervé Pagès wrote:
>> On 03/16/2015 04:06 PM, Michael Lawrence wrote:
>>>
>>>
>>> On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo <robert.castelo at upf.edu
>>> <mailto:robert.castelo at upf.edu>> wrote:
>>>
>>> +1 IMO BioC could adopt the zero-width ranges representation for
>>> insertions, adapting readVcf(), writeVcf(), XtraSNPlocs.*, etc., to
>>> deal with each corresponding beast, be VCF, dbSNP or the like. Who
>>> knows, VCF could also change their representation in the future and
>>> it'll be a headache to update the affected packages if we decide to
>>> keep using its insertion representation internally to store variant
>>> ranges in BioC.
>>>
>>>
>>> That would break just about every tool, so let's hope not. There's a
>>> bunch of code on top of Bioc that currently depends on the current
>>> representation. For example, zero width ranges do not overlap anything,
>>> so they need special treatment to e.g. detect whether an insertion falls
>>> within a gene. There are real benefits to keeping the representation of
>>> indels consistent with the rest of the field (VCF). There was much
>>> thought put into this.
>>
>> Note that findOverlaps() now handles zero-width ranges.
>
>
> predictCoding and locateVariants had to work around the fact that
> findOverlaps didn't work on zero-length ranges. Now that we can handle
> zero-length overlaps this code should be updated (yes, my fault for not
> updating).
>
> How predictCoding and locateVariants currently handle insertions can be
> modified. The current behavior (bug) should not have no bearing on how
> we want to represent indels in the VCF class in general.
>
> I agree with Michael that much thought went into making the VCF class
> consistent with the VCF specs. While information has been added to the
> file format over the years I am not aware of any changes related to the
> positional representation of the variant (ie, it has been stable) and
> think it unlikely this would change in the future.
Just to clarify, my point was that the ranges of the insertions as
currently reported in VCF and VRanges objects cannot be used as-is
in findOverlaps() to detect whether an insertion falls within a gene
or where is falls exactly within a gene. So these ranges need special
treatment like zero-width ranges do.
H.
>
> Val
>
>
>>
>> Straight use of findOverlaps() on the ranges of a VCF object leads to
>> some subtle problems on insertions. For example predictCoding() (which
>> I guess uses findOverlaps() internally) reports strange things for
>> these 2 insertions (1 right before and 1 right after the stop codon):
>>
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>>
>> > cdsBy(txdb, use.names=TRUE)$uc002wcw.3
>> GRanges object with 2 ranges and 3 metadata columns:
>> seqnames ranges strand | cds_id cds_name exon_rank
>> <Rle> <IRanges> <Rle> | <integer> <character> <integer>
>> [1] chr20 [68351, 68408] + | 206100 <NA> 1
>> [2] chr20 [76646, 77058] + | 206101 <NA> 2
>> -------
>> seqinfo: 93 sequences (1 circular) from hg19 genome
>>
>>
>> library(VariantAnnotation)
>> > rowRanges(vcf) # hand-made VCF
>> GRanges object with 2 ranges and 5 metadata columns:
>> seqnames ranges strand | paramRangeID
>> <Rle> <IRanges> <Rle> | <factor>
>> ins before stop codon chr20 [77055, 77055] * | <NA>
>> ins after stop codon chr20 [77058, 77058] * | <NA>
>> REF ALT QUAL
>> FILTER
>> <DNAStringSet> <DNAStringSetList> <numeric>
>> <character>
>> ins before stop codon T TG 70
>> PASS
>> ins after stop codon A AG 70
>> PASS
>> -------
>> seqinfo: 1 sequence from hg19 genome
>>
>> Calling predictCoding():
>>
>> > library(BSgenome.Hsapiens.UCSC.hg19)
>> > predictCoding(vcf, txdb, Hsapiens)
>> GRanges object with 2 ranges and 17 metadata columns:
>> seqnames ranges strand | paramRangeID
>> <Rle> <IRanges> <Rle> | <factor>
>> ins before stop codon chr20 [77055, 77055] + | <NA>
>> ins after stop codon chr20 [77058, 77058] + | <NA>
>> REF ALT QUAL
>> FILTER
>> <DNAStringSet> <DNAStringSetList> <numeric>
>> <character>
>> ins before stop codon T TG 70
>> PASS
>> ins after stop codon A AG 70
>> PASS
>> varAllele CDSLOC PROTEINLOC
>> QUERYID
>> <DNAStringSet> <IRanges> <IntegerList>
>> <integer>
>> ins before stop codon TG [468, 468]
>> 156 1
>> ins after stop codon AG [471, 471]
>> 157 2
>> TXID CDSID GENEID
>> CONSEQUENCE
>> <character> <IntegerList> <character>
>> <factor>
>> ins before stop codon 70477 245938
>> frameshift
>> ins after stop codon 70477 245938
>> frameshift
>> REFCODON VARCODON REFAA
>> <DNAStringSet> <DNAStringSet> <AAStringSet>
>> ins before stop codon AAT AAT
>> ins after stop codon TAA TAA
>> VARAA
>> <AAStringSet>
>> ins before stop codon
>> ins after stop codon
>> -------
>> seqinfo: 1 sequence from hg19 genome
>>
>> PROTEINLOC, REFCODON, VARCODON, and CONSEQUENCE don't seem quite right
>> to me. Could be that my hand-made vcf is missing some important data
>> needeed by predictCoding() though...
>>
>> H.
>>
>>
>>>
>>> robert.
>>>
>>> On 3/16/15 9:00 PM, Kasper Daniel Hansen wrote:
>>> > There would be a LOT of value in having core packages use
>>> exactly the
>>> > same representation; I don't have any opinion about which one is
>>> > best.
>>> >
>>> > Kasper
>>> >
>>> > On Mon, Mar 16, 2015 at 3:38 PM, Hervé Pagès
>>> <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>> > <mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org>>
>>> wrote:
>>> >
>>> > On 03/16/2015 09:22 AM, Michael Lawrence wrote:
>>> >
>>> > Yes, I think it would make sense for the Xtra package to follow
>>> the
>>> > established convention in VariantAnnotation/VCF.
>>> >
>>> >
>>> > I don't know. I agree it would be nice to use a more consistent
>>> > representation of insertions across the software but I'm not
>>> > convinced we should necessarily follow the VCF way, which is to
>>> > include the base before the event in the ref and alt alleles as
>>> well
>>> > as in the reported range.
>>> >
>>> > Note that there doesn't seem to be any consensus in the broader
>>> > Bioinformatics community either. For example dbSNP and HGVS
>>> report
>>> > the range that corresponds to the 2 flanking nucleotides but they
>>> > don't include these nucleotides in the ref or alt alleles. VCF
>>> does
>>> > the same as GFF3 which says "start equals end and the implied
>>> site is
>>> > to the right of the indicated base" except that VCF wants to
>>> treat
>>> > events that occur at position 1 in a special way. In that case
>>> VCF
>>> > says the base *after* the event should be included (seems like
>>> the
>>> > VCF authors want to avoid both: empty ranges and also ranges that
>>> > start at POS 0). BTW it doesn't seem that
>>> > VariantAnnotation::isInsertion() is aware of that special
>>> treatment.
>>> >
>>> > UCSC uses a zero-width range, and so does the XtraSNPlocs.*
>>> > packages. The advantage of this representation is its simplicity.
>>> > There is no special cases. It also reflects the notion that an
>>> > insertion is a replacement of an empty string with a non-empty
>>> > string. No need to include flanking nucleotides in the
>>> representation
>>> > (which is artificial and distorts the "real" alt allele).
>>> >
>>> >
>>> > H.
>>> >
>>> >
>>> > On Mon, Mar 16, 2015 at 9:16 AM, Robert Castelo
>>> > <robert.castelo at upf.edu <mailto:robert.castelo at upf.edu>
>>> <mailto:robert.castelo at upf.edu> <mailto:robert.castelo at upf.edu>>
>>> wrote:
>>> >
>>> > dear devel people, specially Val and Michael,
>>> >
>>> > Hervé has recently added an annotation package that includes
>>> > non-SNVs variants from dbSNP, it is called:
>>> >
>>> > library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
>>> >
>>> > if you execute the corresponding example you'll see the kind of
>>> > information stored in the package:
>>> >
>>> > example(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
>>> >
>>> >
>>> > if you pay attention to the following case:
>>> >
>>> > my_snps1[1:2] GRanges object with 2 ranges and 3 metadata
>>> columns:
>>> > seqnames ranges strand | RefSNP_id alleles <Rle>
>>> > <IRanges> <Rle> | <character> <character> [1] 22
>>> [10513380,
>>> > 10513380] - | rs386831164 -/T [2] 22
>>> [10519678,
>>> > 10519677] + | rs71286731 -/TTT ref_allele
>>> <DNAStringSet>
>>> > [1] T [2] - ------- seqinfo: 25
>>> sequences
>>> > (1 circular) from GRCh38 genome
>>> >
>>> > you'll see the first variant (rs386831164) is a deletion of one
>>> > nucleotide and the second (rs71286731) is an insertion of three
>>> > nucleotides (TTT).
>>> >
>>> > it struck me that the ranges representing the insertion had an
>>> start
>>> > position one nucleotide larger than then and i contacted Hervé
>>> > thinking that this was a mistake. however, i've learned from
>>> him that
>>> > these are so-called "zero-width" ranges and they actually
>>> allow to
>>> > distinguish insertions from every other type of variant without
>>> the
>>> > need to know anything about the reference or the alternate
>>> allele.
>>> >
>>> > currently, the VCF specification 4.2 (http://samtools.github.io/
>>> > hts-specs/VCFv4.2.pdf page 5) uses the nucleotide composition
>>> of the
>>> > REF column to help distinguishing insertions by including the
>>> > flanking nucleotide of the inserted sequence. As a result,
>>> > VariantAnnotation::readVcf() produces ranges that mimic this
>>> > standard having identical start and end positions leading to
>>> 1-width
>>> > ranges:
>>> >
>>> > fl <- system.file("extdata", "CEUtrio.vcf.bgz",
>>> > package="VariantFiltering") vcf <- readVcf(fl, genome="hg19")
>>> > rowRanges(vcf[isInsertion(vcf), ])[1:2] GRanges object with 2
>>> ranges
>>> > and 5 metadata columns: seqnames ranges strand |
>>> > paramRangeID <Rle> <IRanges> <Rle> | <factor>
>>> > rs11474033 20 [45093330, 45093330] * | <NA>
>>> > 20:47592746_G/GGC 20 [47592746, 47592746] * |
>>> > <NA> REF ALT QUAL FILTER <DNAStringSet>
>>> > <DNAStringSetList> <numeric> <character>
>>> rs11474033 C
>>> > CTTCT 2901.12 . 20:47592746_G/GGC G
>>> > GGC 608.88 . ------- seqinfo: 84 sequences from hg19
>>> > genome
>>> >
>>> >
>>> > table(width(rowRanges(vcf[isInsertion(vcf), ])))
>>> >
>>> > 1 78
>>> >
>>> > i would like to ask whether it would make sense to harmonize
>>> the way
>>> > in which dbSNP insertions and variants are imported into
>>> Bioconductor
>>> > by making VariantAnnotation::readVcf() to produce zero-width
>>> ranges
>>> > for insertion variants. this not a feature request, i only
>>> would like
>>> > to know what whether there is a particular reason not to use the
>>> > available zero-width ranges that seem to be implemented for this
>>> > purpose.
>>> >
>>> >
>>> > cheers,
>>> >
>>> > robert.
>>> >
>>> > _______________________________________________
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>>> <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org>
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>>> >
>>> >
>>> > [[alternative HTML version deleted]]
>>> >
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>>> >
>>> >
>>> > -- Hervé Pagès
>>> >
>>> > Program in Computational Biology Division of Public Health
>>> Sciences
>>> > Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N,
>>> M1-B514
>>> > P.O. Box 19024 Seattle, WA 98109-1024
>>> >
>>> > E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>> <mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org> Phone:
>>> > (206) 667-5791 <tel:%28206%29%20667-5791>
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>>> 667-1319
>>> > <tel:%28206%29%20667-1319> <tel:%28206%29%20667-1319>
>>> >
>>> >
>>> > _______________________________________________
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>>> >
>>> >
>>>
>>>
>>>
>>
>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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