[Bioc-devel] VariantAnnotation::readVcf(fl, seqinfo(scanVcfHeader(fl)) problem

This is a good question. I'm not sure we want seqlevelsStyle() to also
alter the genome value. I think it's a reasonable request but I'd like to
open it up to discussion. I've cc'd a few others for input.

Valerie



On 10/24/14 09:05, Robert Castelo wrote:

hi Valerie,

thanks for the quick fix and updating the documentation, i have a
further question about the seqinfo slot and particularly the use of
seqlevelsStyle(). Let me illustrate it with an example again:


==============
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

## read again the same VCF file
fl <- file.path(system.file("extdata", package="VariantFiltering"),
"CEUtrio.vcf.bgz")
vcf <- readVcf(fl, seqinfo(scanVcfHeader(fl)))

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

## select the standard chromosomes
vcf <- keepStandardChromosomes(vcf)

## since the input VCF file had NCBI style, let's match
## the style of the TxDb annotations
seqlevelsStyle(vcf) <- seqlevelsStyle(txdb)

## drop the mitochondrial chromosome (b/c of the different lengths
## between b37 and hg19
vcf <- dropSeqlevels(vcf, "chrM")

## try to annotate the location of the variants. it prompts an
## error because the 'genome' slot of the Seqinfo object still
## has b37 after running seqlevelsStyle
vcf_annot <- locateVariants(vcf, txdb, AllVariants())
Error in mergeNamedAtomicVectors(genome(x), genome(y), what =
c("sequence",  :
   sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9,
chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19,
chr20, chr21, chr22, chrX, chrY, chrM have incompatible genomes:
   - in 'x': b37, b37, b37, b37, b37, b37, b37, b37, b37, b37, b37, b37,
b37, b37, b37, b37, b37, b37, b37, b37, b37, b37, b37, b37, b37
   - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19,
hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19,
hg19, hg19, hg19

## this can be fixed by setting the 'genome' slot to the values of
## the TxDb object
genome(vcf) <- genome(txdb)[intersect(names(genome(vcf)),
names(genome(txdb)))]

## now this works
vcf_annot <- locateVariants(vcf, txdb, AllVariants())
=================

so my question is, should not seqlevelsStyle() also change the 'genome'
slot of the Seqinfo object in the updated object?

if not, would the solution be updating the 'genome' slot in the way i
did it?

thanks!
robert.



On 10/23/2014 11:14 PM, Valerie Obenchain wrote:

Hi Robert,

Thanks for the bug report and reproducible example. Now fixed in release
1.12.2 and devel 1.13.4.

I've also updated the docs to better explain how the Seqinfo objects are
propagated / merged when supplied as 'genome'.

Valerie


On 10/23/2014 06:45 AM, Robert Castelo wrote:

hi there,

in my package VariantFiltering i have an example VCF file from a Hapmap
CEU trio including three chromosomes only to illustrate its vignette.
i've come across a problem with the function readVcf() in
VariantAnnotation that may be specific of the situation of a VCF file
not having all chromosomes, but which it will be great for me if this
could be addressed.

the problem is reproduced as follows:

===========================
library(VariantAnnotation)

fl <- file.path(system.file("extdata", package="VariantFiltering"),
"CEUtrio.vcf.bgz")

vcf <- readVcf(fl, seqinfo(scanVcfHeader(fl)))
Error in GenomeInfoDb:::makeNewSeqnames(x, new2old = new2old,
seqlevels(value)) :
when 'new2old' is NULL, the first elements in the
supplied 'seqlevels' must be identical to 'seqlevels(x)'
====================

this is caused because although i'm providing the Seqinfo object derived
from the header of the VCF file itself, at some point the ordering of
the seqlevels between the header and the rest of the VCF file differs
due to the smaller subset of chromosomes in the VCF file.

This can be easily fixed by replacing the line:

if (length(newsi) > length(oldsi)) {

within the .scanVcfToVCF() function in methods-readVcf.R, by

if (length(newsi) >= length(oldsi)) {

this is happening both in release and devel. i'm pasting below my
sessionInfo() for the release.

let me know if you think this fix is feasible or i'm wrongly using the
function readVcf(). i'm basically trying to use readVcf() without having
to figure out the appropriate value for the argument 'genome', i.e.,
without knowing beforehand what version of the genome was used to
produce the VCF file.

thanks!!
robert.


sessionInfo()
R version 3.1.1 Patched (2014-10-13 r66751)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices
[6] utils datasets methods base

other attached packages:
[1] VariantAnnotation_1.12.0 Rsamtools_1.18.0
[3] Biostrings_2.34.0 XVector_0.6.0
[5] GenomicRanges_1.18.0 GenomeInfoDb_1.2.0
[7] IRanges_2.0.0 S4Vectors_0.4.0
[9] BiocGenerics_0.12.0 vimcom_1.0-0
[11] setwidth_1.0-3 colorout_1.0-3

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.0 base64enc_0.1-2
[3] BatchJobs_1.4 BBmisc_1.7
[5] Biobase_2.26.0 BiocParallel_1.0.0
[7] biomaRt_2.22.0 bitops_1.0-6
[9] brew_1.0-6 BSgenome_1.34.0
[11] checkmate_1.4 codetools_0.2-9
[13] DBI_0.3.1 digest_0.6.4
[15] fail_1.2 foreach_1.4.2
[17] GenomicAlignments_1.2.0 GenomicFeatures_1.18.0
[19] iterators_1.0.7 RCurl_1.95-4.3
[21] RSQLite_0.11.4 rtracklayer_1.26.0
[23] sendmailR_1.2-1 stringr_0.6.2
[25] tools_3.1.1 XML_3.98-1.1
[27] zlibbioc_1.12.0