User: Sigve Nakken
Sigve Nakken • 50
- Reputation:
- 50
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- Location:
- Norway
- Last seen:
- 2 years, 4 months ago
- Joined:
- 4 years, 4 months ago
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Posts by Sigve Nakken
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... Hi,
I am trying to access the Ensembl Regulatory Build through the biomaRt package, using the following commands:
ensembl_mart <- biomaRt::useMart(“ENSEMBL_MART_FUNCGEN")
ensembl_mart <- biomaRt::useDataset(“hsapiens_regulatory_feature", mart = ensembl_mart)
queryAttributes <- c('regul ...
written 2.3 years ago by
Sigve Nakken • 50
• updated 2.3 years ago by
Thomas Maurel • 750
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... Hi Valerie,
Thanks for the rapid response! Processing one sample at a time, using samples in readVcfAsVRanges, appears to be the approach that works for me. I tried the tabix-approach too, but that one gave strange results (not sure why).
I understand the row-based filtering logic used in filterVc ...
written 3.6 years ago by
Sigve Nakken • 50
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... Hi,
I have successfully used the VariantAnnotation (1.12.9 now) for processing my multi-sample VCF files for some time now. Especially, I have utilized the combination of filterVcf (with prefilters) and readVcfAsVRanges to retrieve sample variant calls from my sequencing projects. I have not been a ...
written 3.6 years ago by
Sigve Nakken • 50
• updated 3.6 years ago by
Martin Morgan ♦♦ 22k
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... How do I access the ID column of the VCF when using readVcfAsVranges?
I cannot seem to find these values in the resulting VRanges object.
best,
Sigve
On 28 May 2014, at 01:01, Michael Lawrence
wrote:
> I think you want to use VRanges. See ?VRanges. You can use
readVcfAsVRanges to get one from ...
written 4.4 years ago by
Sigve Nakken • 50
• updated 4.4 years ago by
Michael Lawrence ♦ 10k
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...
On 28 May 2014, at 14:26, Michael Lawrence
wrote:
>
>
>
> On Wed, May 28, 2014 at 2:42 AM, Sigve Nakken
wrote:
> Hi,
>
> readVcfasVRanges works! Makes life much easier for me. Thanks so
much for the clarification:) It cannot seem to find the FILTER
column in the resulting ...
written 4.4 years ago by
Sigve Nakken • 50
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... Hi,
readVcfasVRanges works! Makes life much easier for me. Thanks so much
for the clarification:) It cannot seem to find the FILTER column in
the resulting DataFrame however, yet i specified this in my
ScanVcfParam object, e.g.:
info_tags <- rownames(info(scanVcfHeader(filtered_vcf)))
vcfpara ...
written 4.4 years ago by
Sigve Nakken • 50
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... Hi,
Ive had similar challenges as Francesco, and have unsuccessfully
tried to use the data structures and functions provided by
VariantAnnotation. My experience is that I need the expand'
functionality more often with respect to the samples rather than the
annotation tags. And as my experience wi ...
written 4.4 years ago by
Sigve Nakken • 50
• updated 4.4 years ago by
Michael Lawrence ♦ 10k
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