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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61 views

Supplementary aligments in VAF

I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot. I'm interested in what is done generally, if there is a "rule" ...
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Can we use reference strain as an out-group strain to root SNP based species tree?

I have generated a species tree based on whole-genome SNP using CSI_SNP_Phylogeny, wherein I used Reference strain as an outgroup to root my species tree (SNP fasta were downloaded and RaxML used to ...
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FMT/DP of missing genotypes in bcftools

I have a VCF file where the FMT/DP of missing genotypes has been recorded itself as missing data (".") When I filter ...
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29 views

Filtering samples by FORMAT attributes using bcftools

The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
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20 views

How to assess how prone genes may be to acquire structural polymorphisms?

I have 5 strains of P.falciparum. Each FASTA file has all its annotated CDSs. After a first pre-processing phase, where I eliminated the strangest sequences (perhaps the longest or shorter ones, which ...
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15 views

How do I infer someone's haplotype of a gene from data on several of the gene's SNPs?

For a a few SNPs from given gene, I know there happen to be several haplotypes that most of the population has. But from a person's data on those SNPs, we have two alleles at each SNP, so it's not ...
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21 views

freebayes segmentation fault

I have a draft, Illumina-based, genome and bunch of reseq samples. I generated bam files using bowtie2 and marked duplicates using ...
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50 views

Biology behind PCA analysis based on SNP

What is the biology behind SNP based PCA analysis to study population structure? I am reading some articles where they used PCA analysis to compare isolates of drosophila that is collected from a ...
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20 views

How to control/normalize for number of reads when calling SNPs using RNA-Seq?

I used the GATK pipeline to call SNPs on males and females using RNA-Seq data. But the males have a higher read count (~43-46M reads) than the females (~40-42M reads). This causes SNP counts to be ...
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What number to give for `-ploidy` for durum genome in GATK?

I have some genome sequencing data from durum wheat. I'm using GATK to call variants. I got the genome sequence here: http://plants.ensembl.org/Triticum_turgidum/Info/Index Here is the reference ...
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1answer
33 views

Random GWAS data generator

I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
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35 views

RAD Seq Data Analysis without barcode

I received a ddRAD Seq data from my supervisor without barcodes and restriction enzymes. I asked him for both and he said I don't need it since the data has been cleaned by the company. Now, I am ...
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20 views

Loss of predictive power of polygenic risk score when dataset contains missing variants

I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
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41 views

Apply trained PRS on another dataset

I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set. Once I compute the PRS I get a ...
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1answer
28 views

dbnSNP frequency anomalies

Sometimes dbSNP reports very different allele frequencies for different large-scale genome projects e.g. between 1000 Genomes and GnomAD rs11822440 1000Genomes A=0.4629 C=0.5371 GnomAD A=0.99997 ...
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16 views

GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
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1answer
34 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 ...
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45 views

Odds ratio and enrichment of SNPs in gene regions?

I did a QTL analysis with a panel of 7M SNPs, and want to analyze the enrichment of the significant qtl-SNPs in different genic regions (promoters, gene bodies, TFBS, etc.). A straightforward way to ...
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1answer
25 views

Core genome too short

I'm trying to create a snp distance matrix from M tuberculosis isolates to try and infer transmission networks. My plan was to use snippy to make a core genome ...
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2answers
54 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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85 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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19 views

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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25 views

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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55 views

Global SNP frequency database?

Is NCBI's 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. For example, on average, ...
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50 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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1answer
45 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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38 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
109 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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1answer
60 views

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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47 views

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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49 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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49 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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42 views

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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1answer
27 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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122 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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2answers
54 views

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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1answer
104 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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31 views

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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2answers
69 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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1answer
37 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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106 views

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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1answer
24 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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975 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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205 views

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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328 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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2answers
147 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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128 views

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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2answers
248 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 ...