Questions tagged [snp]
Single Nucleotide Polymorphisms. How to find them? How to correlate them with other data? How to represent them? What is their distribution?
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Best Approach for Translating Aligned Population Sequences to Detect Single Amino Acid Variations?
I have a set of population sequence files that I've already aligned, identifying all existing SNVs (A, C, T, G, del) within each population, while excluding inserts and non-singular deletions.
I now ...
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How do I infer sex from a VCF file?
I have human samples VCF files that I want to infer the sex of. I do not have sequencing information or information about coverage. What's the best way to go about this? I'm looking for a robust and ...
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How to interpret mutagenesis results from pymol to make conclusions about structural/functional changes and predict resulting pathogenesis?
I'm a beginner bioinformatics student. I am currently working on my first project. We have gathered data about SNPs that are associated with a particular disease. We aim to understand the functional ...
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Nucleotide diversity and TajimaD from SNPs
This question was also asked on Biostars
I have the illumina paired end reads of four chromosomes in fastq format. Using the cat command, I merged all of the fastq files into one. I used the GATK hard ...
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How to Call SNPs from Assembled Fasta Files?
I have experience in obtaining a variant calling file from NGS sequencing files using the Samtool/bedtools workflow. However, when we receive pre-assembled sequences, it becomes challenging to apply ...
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Fixation index calculation from the vcf files
I used the Python script FSTest (https://github.com/similab/FSTest) for the calculation of the fixation index from the extracted SNPs. I used the following command:
...
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Replicating VCF Filtering & Trait-Based SNP Extraction Workflow
I'm new to handling SNP genotyping data in VCF format.
My goal is to identify significant SNPs linked to a specific trait (like "height") for specific samples in a multi-sample VCF file. My ...
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GBS- 'Failure' in, Per base sequence content, Sequence Duplication Levels, and Adapter Content
I have a GBS sequence on the Illumina platform that in the FASTQC quality report has “Failure” in : Per tile sequence quality, Per base sequence content, Sequence Duplication Levels and Adapter ...
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Approach for manually adding genotype of two SNPs to plink files for 350 people?
I have a data set of ~350 humans, genotyped on an Illumina. I have bed, bim, and fam files for them. Because of difficulty genotyping them, the genotyping does not include rs7412 or rs429358. However,...
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SNP Signatures with Limited WGS Data:
On 80 WGS samples, I'm dissecting SNP signatures linked to milk production in a scarcely studied animal. Post-variant calling and QC association analysis have been tricky. I'm here to tap into our ...
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How should multi allelic sites be handled in calculation per site Fst?
I'd like to calculate per site Fst(fixation index) to investigate genomic differentiation between two populations(haploid).
I did SNP calling and got vcf file.
In the vcf file, multi allelic sites ...
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Different ClinVar classifications/SNPs are linked to the same rsid
I am using R to extract ClinVar classification of SNPs using rsid. Here's an example of my workflow:
Patient data:
Sample
Func
Gene
Codon_Change
dbSNPv151_GRCh38
Chr
Start
End
Ref
Obs
Mary
...
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Does using a microarray chip that matches the chip used in training lead to higher explained variance of a polygenic score?
I'm trying to replicate an existing polygenic score (i.e. test the accuracy in a new sample), and want to know if matching the original study's microarray chip will improve the accuracy (that is, ...
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SNP How to detect regions of erratic pairwise alignment?
I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations.
As the mutations aren't known, those clusters of sequences were pairwise-...
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Why does my HWE QQ plot have extreme deviation and what does it mean?
This question was also asked on Reddit
I have recently completed my thesis and one of the comments was that I report on why this graph looks this way. I have tried to find a reason but the closest I ...
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Feasible to find genetic variations of two samples using RNAseq data?
I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL.
The former expresses a Ptprc-b allele and the latter expresses a ...
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Extracting information from VCF file for many specific positions in specific chromosomes?
I have an excel file that I created from VCF file for common SNPs across 6 samples. This excel have the chromosomes and the position of the SNPs only (see example table1)
Now I would like to obtain ...
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Getting VCF file that contain common SNPs from 6 VCF file using isec
I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command
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How do you go about grabbing proper genotyping infomation from dbSNP using entrez API?
I made an R function to grab rsID genotypes from dbSNP using the entrez API. For example, here is the xml output that I am trying to parse:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=...
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How can I detect the Apo B gene mutations in my raw dna data?
Familial defective apolipoprotein B-100 (FDB) is an autosomal dominant disorder associated with increased plasma cholesterol concentration and may thus increase the risk of premature coronary heart ...
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When it is stated in your consumer genetics testing report that you have x% (lets say 1.3 percent...) Neanderthal DNA, what is actually meant?
This question has also been asked on Biology SE
When a raw number like 1.3 percent is stated, it is confusing without context,and can be misinterpreted. So does 1.3 percent mean that 1.3 percent of ...
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Can you infer orientation from vcf file data?
I have a dante labs dataset that I would like to cross reference with SNPedia but I am unclear about orientation. I've read the info on SNPedia and other places about it but I just don't get it yet. I ...
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Variants list to aminoacids
I have the sequencing data of a Monkeypox virus sample. I have the list of variants extracted from Nextclade and I want to find the corresponding aminoacids substitution.
For example I have the ...
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Help with analyzing SNP data for three patient groups
I am currently working on a project where I have genetic data for patients classified into three different groups. Specifically, I have information on 26 SNPs for each patient. I have recorded each ...
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SKAT method in R
I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.
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Project PLINK eigenvector from one group on top of another group
I have 1 .bcf file called with individuals from two groups, one which is my samples, another which is a reference panel. Due to my samples having a limited amount ...
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Converting a Dante Lab VCF file
Is there an easy way to grab the rsids (hg38) of a VCF file? I know one of the tabs can contain RSIDs, but this file doesn't contain any.
I have a software I created for mapping 23AndMe DTC testing to ...
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Getting nearest gene from SNP data using SNP ID, CHR, and BP
I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
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Arlequin - How to assign samples to populations?
I have converted a VCF file to the arlequin file format. It consists of 20 samples that should belong to three populations, along with a few thousands SNPs. However, when I load the arlequin file into ...
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Retrieve rsIDs from chromosome positions using MRutils::get_rsid_from_position
I have 5609 chromosome positions with both ref and alt alleles. I want to retrieve rsIDs for the same. I tried get_rsid_from_position() of the ...
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VCF: false insertions?
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret or handle. An example (selected samples from a huge vcf):
<...
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Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9
I downloaded the following vcf file from https://www.internationalgenome.org/.
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502....
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SNPs location out side the gene
I downloaded exome data from gnomad to get the allele frequency of some SNPs that I'm analyzing. The SNPs are from external resource. Some SNPs (in my data) are not present in the exome data (in ...
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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 ...
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Find SNPs in yeast genomes
I'm a new Bioinformatic scientist working for a yeast genetics company.
Objective To create a database of yeast genomes from NCBI and identify SNP variants.
In my pipeline
FastQC,
Trimmomatic,
BWA
...
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SNPs with high population differentiation from 1k Genome dataset
I am trying to reproduce the results from this paper "Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences".
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Converting from VCF to PLINK while maintaining the SNP names from the VCF file
Just as the title says, I am working in PLINK 1.9 trying to convert the following VCF into a PLINK file (binary or not either is fine), while maintaining the SNP names from the VCF file. I am on ...
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What tool I can use to map short-reads sequences to reference genome and get specific mapped size
I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.
Anyone knows what bioinformatics tool I can ...
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Weird data in VCF file
I am using GATK HaploTypeCaller for SNP calling. I have 300 samples. As far as I understand that if a sample is missing a SNP it should be denoted by ./., however, I am getting a lot of values like 0/...
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BAM files with no RNAME and POS, how to map contents to SNPs?
I have a set of 4 .bam files containing the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with ...
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Imputing small region of the genome
If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' ...
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Reference variant detected as altered one in bam file
I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer ...
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Regression plot of a continuous trait - is there a binary equivalent?
Within the GWAS wikipedia page, you can view the following plot:
"Illustration of a simulated genotype by phenotype regression for a
single SNP. Each dot represents an individual. A GWAS of a ...
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RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias
I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters.
Aim We would like to conduct SNP discovery of these samples.
...
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Confusing result from Sanger Imputation Service (Eagle v2.4 for phasing, PBWT v3.1 for imputation)
I ran my 23andMe data through the Sanger Imputation Service that uses Eagle v2.4 for phasing, PBWT v3.1 for imputation.
However, some aspects of the results are very confusing to me. Perhaps see #3 (...
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Assess ploidy estimation through SNV and CNV results
I want to assess ploidy estimation (i.e., diploid vs tetraploid) in a set of samples for which I have both results from the variant caller (i.e., SNVs) and from the copy number caller.
What are the ...
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SNPs in LD in which populations?
I have 3 SNPs that are in LD in 'several' populations here:
https://www.ebi.ac.uk/gwas/variants/rs13078854#ld_panel_label
It's a pain to look at all (30) populations one by one to manually check if ...
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Filtering a vcf with a text file of SNP rsIDs
I have a vcf file containing an ID field with a snps and a list of human SNPs from dbSNP.I want to remove whatever in dbSNP from vcf file. The text file is like this:
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Extracting a column from a vcf file
I have a zipped vcf file of dbSNP hg38 version
No space left on my device to unzip that
I want to extract a column from that
I have tried this
...
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imputed dosage values for vcf files
I have one more question related to genotype file. I submitted the job in michigan imputation server.
and my imputed dosage for chr 22 file is:
22 16050435 22:16050435:T:C T C . PASS
AF=0.00098;MAF=0....
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