Questions tagged [variants]
The variants tag has no usage guidance.
13
questions
2
votes
1answer
28 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
2answers
80 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. ...
2
votes
0answers
32 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 ...
0
votes
1answer
109 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:
...
7
votes
1answer
43 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
1answer
68 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 ...
0
votes
0answers
7 views
How to generate variant DNA sequence from an HGVS-formatted variant?
I'm parsing clinvitae using the python hgvs module. For each variant, I want to generate the variant DNA sequence in a 500 bp radius around the variant position. I don't see a way to generate the ...
0
votes
1answer
35 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 ...
2
votes
2answers
125 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. ...
1
vote
1answer
63 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
1answer
72 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
2answers
51 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
0answers
42 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 ...
