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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29 views

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

I want to add the frequencies of the genotypes to a baseline of raw DNA data I've got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all). All in build 37 human genome. ...
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27 views

Convert VCF to genotype table

How can I convert a VCF file into a genotype table (SNP matrix)? I have this format: ...
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e-utils api: get chromosome position for each snp on a gene

So I have the following e-utils api-link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json it returns all the SNP-ids for the gene with ...
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How can I extract all known mutations of my BAM (or SNP/INDL files)?

I am using a Genome Explorer tool to see all the mutations on my own DNA. My particular interest is on listing the variants and get their names/ids. Here are a few screenshots: You can see that ...
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34 views

Global SNP frequency database?

Is dbSNP the most comprehensive database of SNP frequency? I'd like to get the largest possible database of allele frequencies per 'population' or geographic region. e.g. On average, which country ...
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25 views

Understanding snpSift/snpEff output

I am trying to check the concordance between two VCF files. Each file contains the same samples, with one being a sequencing experiment, and the other having been genotyped by SNP array. I used snpEff/...
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General question: How to assign my SNP (Wheat, Illumina 15K) to specific chromosomes?

I have 2000 lines of wheat genotyped with a 15K illumina chip. I also have the name of the SNPs. I would like to know how could I find out which SNPs are in each chromosomes.
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34 views

Database of RNA-Seq and SNP genotyping data

I need to obtain publicly available RNA-seq + SNP genotyping data for a cohort - ideally one where the RNA-seq data has been sequenced from brain tissue. I have found CMC and GTEx to be sufficient ...
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33 views

How to analyze co-occurrence of multiple SNPs?

I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 ...
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36 views

Subsetting SNPs with specific exclusion criteria using bcftools

I am trying to subset SNPs from 32 cultivars. I have the following exclusion criteria: >20% missing data SNPs present in less than 50% of genotypes Each genotype must have at least 50% of included ...
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1answer
79 views

Allele count is zero

I ran freebayes on bacterial data and got a vcf file. Some of the SNPs found have AC=0, but in the bam file I can see that there are alternative alleles, so in my ...
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How can I download the SNP genotyping information from GTEX?

I am new to the field of Bioinformatics. GTEx database is great; I know how to check whether a SNP is eQtl with the online tools of GTEx. But my question is how to download the right data to draw a ...
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REMC SNP annotations for transcriptome prediction - epiXcan

I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper: https://www....
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40 views

How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

For easier management of a database of dna profiles, I'm creating a tool to perform one-to-one matching on two profiles with snp genotype information. Basically, something that works similar to ...
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44 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 ...
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Variant calling for a subset of genes using whole gneome sequencing data

I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone ...
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Bcftools call always assigns a genotype even if there are no reads?

I am variantcalling my 96 multi sampled bam file with samtools/bcftools however I obtain some strange results. When I use the following command: ...
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25 views

How to Convert From Gene Location to SNP Location

I am new to this. I have an SNP array composed of digits [0,1,2] for chromosome 21. How do I find the start:end locations for the region that is "21q22.11" step by step?
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Common QC parameters for SNP chip data in PLINK

How do you set QC measurements? Seems very subjective. Is there a right way to set: 1) individual call rate, 2) SNP call rate, 3) minor allele frequency (MAF), and 4) linkage disequilibrium (LD) in ...
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62 views

Running IBD using PLINK --parallel (v2)

I have merged two huge .gen files with roughly 500k samples in total - around 3 TB. I wish to run an IBD (identity by descent) check to identify if there are ...
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Questions regarding the detection of variants (SNPs and Indels) in mammal

Greetings, I’m a newbie in bioinformatics working currently on my first project regarding detection of variants (SNPs and Indels) in mammal assembly genome. I used the following method to detect ...
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73 views

Simulating phenotype with the 1000 Genomes Project

I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use ...
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How to segment genome into homozygote/heterozygote blocks based on RNA-Seq data

Given a RNA-Seq data of a progeny between two inbred lines (for example an F4 plant which was derived from two inbred lines (parents) and the F1 selfed 3 times; however this is probably not crucial ...
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61 views

1000 genomes missing SNPs on chr X in GRCh38

I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant ...
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33 views

significant SNPs to annotated candidate genes

I have performed GWAS and got some significant SNPs. How can I get candidates genes in the flanking regions of those SNPs and also their functional annotations (eg. KEGG).
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How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
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23 views

Store and search on variant and annotation data

I need to store a large number of variants with their annotations. I need to import dbSNP, as well as Clinvar, and ExAC etc. Also I have sample variant data from patients. I need to be able to search ...
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680 views

What does PCA mean on GWAS

I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means. So let's say I have 100,000 ...
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Extracting the number SNP in each range

I have called copy number and I have 2 files (I have shared the link of my files ); One contains some ranges ...
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194 views

How to compute LD for pairs of variants with Plink

I have a set of SNPs (single nucleotide polymorphisms) { S1, S2, ..., SN } from approximately 200 humans. I wish to determine the linkage disequilibrium (LD) for a defined subset of these SNPs. By ...
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141 views

Variant calling without matched normal sample

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), ...
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GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
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236 views

Selecting 65000 SNPs where AF is close to 0.5 in all or most populations

I am evaluating the tool somalier (https://github.com/brentp/somalier) and I need to create a list of about 65,000 SNPs where the allele frequency (AF) is as close to 0.5 as possible across the most ...
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63 views

Calculate average parental genotype

I am interested in creating an averaged value for genotype across two parents: E.g. Input (three unrelated couples, 1, 2 and 3): ...
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2k views

SNP vs Point Mutation

What is the difference between a Single Nucleotide Polymorphism (SNP) and a point mutation? I am quite confused in understanding these term as both of them refer to one base difference from the ...
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R package grur: missing_visualization() fails during redundancy analysis of .vcf

I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it ...
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ncbi…eutils/esearch.fcgi: How to search now in the snp database?

According to the 2017(!) textbook, it worked at that time, for instance, https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism At ...
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357 views

Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
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213 views

calling diploid SNVs from long reads

I'd like to call diploid SNV variants from long-reads data (~80SMRTcells PacBio). I have generated a draft reference genome for an indivudual from a heterozygous (~4%) species (Canu+Haplomerger2). ...
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118 views

Using Beagle 4.1 for phasing and IBD - chromosomes

I am trying to use beagle 4.1 for phasing and IBD analyses. I was wondering if I need to run the analysis by chromosome or I can put them together in the same vcf file.
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101 views

chromPlot R package: remove scales

I am using chromPlot R package to plot some SNPs and their associated score, however, I cannot find a way to remove the scale of such score (circled in the attached picture). Does anybody know how to ...
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90 views

Reference genome for allele specific expression

We are trying to sort out a pipeline for doing allele specific expression. Our plan is to call SNPs from RNA-seq data and combine with known SNP annotations. A well known problem in ASE is reference ...
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1answer
78 views

Understanding SNP coding for association analysis

I'm working on a project about detecting SNP association with a disease. As I understand, SNP is a single variation of the nucleotide that occurs for more than 1% of the population. So, if a gene is ...
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50 views

using SNPs to identify mixed samples

Is there a way to identify mixed samples based on SNPs? Example input (table of genotypes for multiple samples): ...
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106 views

Sampling haplotypes

I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project. I want to simulate different whole genomes i.e generate a new population by ...
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50 views

case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
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66 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
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56 views

Associating SNP and GENE

Assuming I have SNPs data using hg19, how can I know which SNP belongs into which Gene? The data looks like: chr10_103577643 chr10_124712463 and so on. I ...
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88 views

Use of heterozygous SNPs in cancer research: why?

When reading about allelic fraction (AF) and SNPs in cancer research, they always mention the fact that they're using heterozygous SNPs (informative SNPs). Why is this? Why can't we use homozygous ...
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Statistical approach to compare the SNP genotyping data among set of individuals

So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry. ...