Questions tagged [variants]

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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 : <...
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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 ...
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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 ...
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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 : ...
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2 answers
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Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

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 ...
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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....
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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 ...
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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. ...
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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 ...
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1 vote
1 answer
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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: ...
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7 votes
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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, ...
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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 ...
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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 ...
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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 ...
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2 votes
2 answers
235 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. ...
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1 answer
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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 ...
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2 votes
1 answer
187 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 ...
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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 ...
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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 ...
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