[Bioc-devel] proposal for additional seqlevelsStyle
Kasper Daniel Hansen
k@@perd@n|e|h@n@en @end|ng |rom gm@||@com
Fri Dec 13 19:51:20 CET 2019
If the chromosome name depends on the assembly, that makes GenomeInfoDb
even more useful and necessary. Provided it is supported of course.
On Fri, Dec 13, 2019 at 11:45 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:
> I tried an inline png but I think it was rejected by bioc-devel. Here's
> another try.
>
> On Fri, Dec 13, 2019 at 11:40 AM Vincent Carey <stvjc using channing.harvard.edu
> >
> wrote:
>
> > Thanks -- It is good to know more about the complications of adding
> > seqlevelsStyle elements.
> > I am not sure how pervasive this will be in SNP annotation in the future.
> > The "new API" for dbSNP
> > references SPDI annotation conventions.
> >
> > https://api.ncbi.nlm.nih.gov/variation/v0/
> >
> > at least one dbsnp build 152 resource uses this nomenclature. The one
> >
> > referenced below is the "go-to" resource for current rsid-coordinate
> >
> > correspondence, as far as I know.
> >
> >
> > > library(VariantAnnotation)
> >
> > *0/0 packages newly attached/loaded, see sessionInfo() for details.*
> >
> > > mypar = GRanges("NC_000001.11", IRanges(100000,120000)) # note seqnames
> >
> >
> > > nn = readVcf("
> >
> ftp://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.38.gz
> > ",
> >
> > + genome="GRCh38", param=mypar)
> >
> >
> > > head(rowRanges(nn), 3)
> >
> > GRanges object with 3 ranges and 5 metadata columns:
> >
> > seqnames ranges strand | paramRangeID
> REF
> >
> > <Rle> <IRanges> <Rle> | <factor>
> <DNAStringSet>
> >
> > rs1331956057 NC_000001.11 100000 * | <NA>
> C
> >
> > rs1252351580 NC_000001.11 100036 * | <NA>
> T
> >
> > rs1238523913 NC_000001.11 100051 * | <NA>
> T
> >
> > ALT QUAL FILTER
> >
> > <DNAStringSetList> <numeric> <character>
> >
> > rs1331956057 T <NA> .
> >
> > rs1252351580 G <NA> .
> >
> > rs1238523913 C <NA> .
> >
> > -------
> >
> > seqinfo: 1 sequence from GRCh38 genome; no seqlengths
> >
> >
> > On Fri, Dec 13, 2019 at 11:01 AM Robert Castelo <robert.castelo using upf.edu>
> > wrote:
> >
> >> hi Hervé,
> >>
> >> i didn't know about this new sequence style until Vince posted his
> >> message and we briefly talked about it at the European BioC meeting this
> >> week in Brussels. however, i didn't know that the style was specific to
> >> a particular assembly. i have no use case of this at the mome moment,
> >> i.e., i have not encountered myself any annotation or BAM file with
> >> chromosome names written that way, so i don't know how pressing this
> >> issue is, maybe Vince can tell us how spread such chromosome naming
> >> style may become in the near future.
> >>
> >> naively, i'd think that it would be matter of adding a
> >> reference-specific column, i.e., 'GRCh38.p13', 'GRCh37.p13', etc., but i
> >> can imagine that maybe the "reference style" concept might not be the
> >> appropriate placeholder to map all different chromosome names of all
> >> different individual human genomes uploaded to NCBI. maybe we should
> >> wait until we have a specific use case .. Vince?
> >>
> >> robert.
> >>
> >> On 12/11/19 10:06 PM, Pages, Herve wrote:
> >> > Hi Vince, Robert,
> >> >
> >> > Looks like Vince wants the RefSeq accession e.g. NC_000017.11 for
> chrom
> >> > 17 in the GRCh38.
> >> >
> >> > @Robert: Is this what you're also interested in?
> >> >
> >> > The problem is that the RefSeq accessions are specific to a particular
> >> > assembly (e.g. NC_000017.11 for chrom 17 in GRCh38 but NC_000017.10
> for
> >> > the same chrom in GRCh37).
> >> >
> >> > Currently seqlevelsStyle() doesn't know how to distinguish between
> >> > different assemblies of the same organism. Not saying it couldn't but
> it
> >> > would require some thinking and some significant refactoring. It
> >> > wouldn't be just a matter of adding a column to
> >> > genomeStyles()$Homo_sapiens.
> >> >
> >> > H.
> >> >
> >> >
> >> > On 12/10/19 14:19, Robert Castelo wrote:
> >> >> I second this, and would suggest to name the style as 'GRC' for
> "Genome
> >> >> Reference Consortium".
> >> >>
> >> >> thanks Vince for bringing this up, being able to easily switch
> between
> >> >> genome styles is great.
> >> >>
> >> >> if 'paste0()' in R is one of the most influential contributions to
> >> >> statistical computing
> >> >>
> >> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__simplystatistics.org_2013_01_31_paste0-2Dis-2Dstatistical-2Dcomputings-2Dmost-2Dinfluential-2Dcontribution-2Dof-2Dthe-2D21st-2Dcentury&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc&s=b0_SIu8orJ7ZcCS3TIodFvGTPibt9R8vFL5Y40YSx3Q&e=
> >> >>
> >> >> i think that 'seqlevelsStyle()' from the GenomeInfoDb package is one
> of
> >> >> the most influential contributions to human genetics, if you think
> >> about
> >> >> the time invested by researchers in parsing and changing between
> >> >> different styles of chromosome names :)
> >> >>
> >> >> robert.
> >> >>
> >> >> On 06/12/2019 15:03, Vincent Carey wrote:
> >> >>> I raised this issue previously with little response.
> >> >>>
> >> >>> I'd propose that we add a column or two to
> genomeStyles()$Homo_sapiens
> >> >>>
> >> >>>> head(genomeStyles()$Homo_sapiens, 2)
> >> >>> circular auto sex NCBI UCSC dbSNP Ensembl
> >> >>>
> >> >>> 1 FALSE TRUE FALSE 1 chr1 ch1 1
> >> >>>
> >> >>> 2 FALSE TRUE FALSE 2 chr2 ch2 2
> >> >>>
> >> >>>
> >> >>> that includes the values for "NCBI reference sequence names"
> >> >>>
> >> >>> See
> >> >>>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_nuccore_568815581&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc&s=3Jy-MH7heIcrc_A4qm_izduLvBoPWHSeq4gdxf5nv24&e=
> >> >>> for one report on chr17,
> >> >>> and
> >> >>>
> >> >>>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F000001405.39&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc&s=y6ut_Xcc4rSbXanckiJhiwLsL0W8neJfKWQa6wnG3aM&e=
> >> >>>
> >> >>> for a table that includes the Genbank labels.
> >> >>>
> >> >>> Should I just file a PR at
> >> >>>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomeInfoDb_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc&s=KMzfo3_8kkJ-wdvRCNP5rUjTVMW87brj07yHaKL5Qb0&e=
> >> >>> after
> >> >>> testing?
> >> >>>
> >> >>
> >> >> _______________________________________________
> >> >> Bioc-devel using r-project.org mailing list
> >> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc&s=SvtNreKVOHnSGjsRwzWWpttpEF7wBXI5utI37-qgX1A&e=
> >> >>
> >> >
> >>
> >> --
> >> Robert Castelo, PhD
> >> Associate Professor
> >> Dept. of Experimental and Health Sciences
> >> Universitat Pompeu Fabra (UPF)
> >> Barcelona Biomedical Research Park (PRBB)
> >> Dr Aiguader 88
> >> E-08003 Barcelona, Spain
> >> telf: +34.933.160.514
> >> fax: +34.933.160.550
> >>
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:15}}
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