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Questions tagged [variants]

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4 votes
1 answer
65 views

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 ...
1 vote
0 answers
39 views

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 ...
2 votes
1 answer
881 views

Compare VCF files

I have two strains, X and Y, and I would like to compare the variants found in both. I have my own parent strain, Z, that was sequenced and assembled to be used as the reference genome. I first ...
2 votes
1 answer
58 views

Standardizing Variant IDs best practise

I'm currently pondering on the best approach to handle and standardize variant IDs within our department to mitigate the challenges associated with rsids and the potential ambiguity of just using ...
1 vote
0 answers
29 views

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 ...
0 votes
0 answers
40 views

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, ...
4 votes
1 answer
267 views

How to get a GISAID account? I registered months ago, still no reply!

Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance. However, I cannot seem to get access to GISAID, the platform ...
0 votes
0 answers
20 views

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 ...
1 vote
1 answer
1k views

Find common SNPs in multiple VCF files

I have 3 VCF files. A1.vcf A2.vcf A3.vcf I want to get the common SNPs that are present in all these three files. And output must be in vcf format. output: ...
3 votes
3 answers
275 views

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these? For the moment I ...
1 vote
1 answer
60 views

Name this alternative INDEL format

I have recently been working with variants which are represented in a non-standard format. This alternative format uses a period instead of prefixing variants with a reference base. What is this ...
1 vote
0 answers
345 views

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 ...
0 votes
1 answer
70 views

syndip dataset for benchmark variant

I have a question about syndip dataset : https://github.com/lh3/CHM-eval . I'm struggling to find the syndip vcf. In the release ( https://github.com/lh3/CHM-eval/releases ), we have a file named : <...
0 votes
0 answers
181 views

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 ...
5 votes
0 answers
53 views

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 ...
1 vote
1 answer
270 views

Dictionary and index of vcf for base recalibration step

I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://console.cloud....
3 votes
1 answer
54 views

pathogeniticy prediction tool

I have a question related to the evaluation of variant pathogenicity in the context of human genetics. There are many predictors available, however, is there a specific predictor that takes into ...
1 vote
0 answers
41 views

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 : ...
2 votes
1 answer
65 views

Counting the co-occurrence of variants A and B in an aligned sequencing read

I need some help getting started on this project. To simplify we want to be able to quantify the occurrence of 3 variants on each sequencing read in an alignment file as a proxy measurement for ...
0 votes
2 answers
712 views

Remove repetitive region vcf file using repeatmasker bed file [duplicate]

I have a 1000 genomes vcf file for chromosome 14. And I want to remove variants in repetitive regions flagged by repeatMasker. I have a bed file for those repeats. I downloaded that file from UCSC. ...
7 votes
1 answer
49 views

How to represent random sequence elements in SBOL?

In our lab, we work with synthetic biology components with partially random sequences (similar to work in directed evolution). So, for example, we have a plasmid design with several components, ...
1 vote
1 answer
290 views

genotyping or variant calling in R

Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions. I found deepSNV::bam2R which roughly does what I ...
2 votes
2 answers
563 views

Produce .vcf file of ALL mutations in .bam file

I got tasked with a problem, that i thought would be quite simple to solve, but turned out to be quite tricky. Our lab is running targeted mutagenesis experiments in yeast using crispr base editors. ...
0 votes
1 answer
41 views

Inheritance annotation for nsSNPs

I am relatively new to SNP analysis. Is there a database to find annotation about the Mendelian inheritance of SNPs? I have a small list of nsSNPs (non-synonymous SNPs) and I need to find how they are ...
1 vote
1 answer
70 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
2 votes
1 answer
415 views

SNPEFF genome build with specific codon usage

Failing to build my own Arabidopsis thaliana reference with Mt using 'codon.Mitochondrial' and Pt using 'codon.Bacterial_and_Plant_Plastid' but the same commands works well with both lines with codon ...
0 votes
2 answers
74 views

Q: What analyses can I perform with a completely phased genome assembly?

Phasing a genome is the process of determining which variants lie on which copy of each chromosome. For example, position 5,430,500 might have an A on the paternal chromosome, but a T base on the ...
1 vote
0 answers
69 views

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 ...