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Questions tagged [variants]

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Parse RNA variant effect annotations ("r." format)

I've got annotations for splicing variants in a format like this (this is one variant): Variant: NM_004092.3:c.88+5G>A Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23) I want to extract ...
Ron's user avatar
  • 51
4 votes
1 answer

Identifying somatic mutations in cell lines

I would like to identify the somatic mutations present in a cell line and characterise the genes that are potentially affected by those mutations. For example, are there oncogenes mutated in a ...
Macintosh's user avatar
  • 160
1 vote
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how to annotate the effect of a genomic variant to predict what the resulting protein is?

Spoiler: This is probably a theoretical question. But, of course, if you have any tool that does this I will be extremely happy. So, I have WGS data for an organism O, both wild type (WT-O) and ...
gabt's user avatar
  • 348
1 vote
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How to make a POST "vep/:species/region" request that is able to accomodate multiple alternate alleles for a single variant?

There is an R code example on Ensembl's website on how to execute a POST "vep/:species/region" request for variants that only have one alternate allele. The part that holds the variant data ...
Derk's user avatar
  • 11
1 vote
0 answers

HGVS python package : How to parse complex insertions?

In HGVS package, how to create more complex variants ? I just wonder how can I parse more complex insertions such as those : ...
jossefaz's user avatar
  • 111
1 vote
0 answers

About getting rs id from chromosome and position

Hi I have a dataset with chromosome and position. VARIANT_ID chromosome position 17_26797415_147499 17 26797415 17_26797556_147500 17 26797556 How can I ...
susuauidikd's user avatar
1 vote
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Filtering out 8-oxoG-derived artefacts in variant calls from cfDNA

I have cfDNA samples which were sequenced (at about 300-1000X) on a 30-gene panel via a capture-seq protocol for the purposes of calling variants on circulating tumour DNA. However, the resulting ...
user36196's user avatar
  • 291
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spliceAI not giving output value while running using vep (Variant Ensemble Predictor)

While generating the predictions using spliceAI from vep, I am not getting any values. I used this command to generate the output, ...
Sruthi's user avatar
  • 1
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What statistical analysis should I perform on DNA variants from unequal number of case (34) and control (11) samples?

I have performed NGS on 34 patient samples and 11 controls. Now I have variants from both groups but there is obvious difference in number of variants. How can I compare variants of both groups ...
Malik Saad's user avatar
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0 answers

Extract SNPs from multiple sequence alignment

I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
ksw's user avatar
  • 111