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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Extract read names and the associated nucleotides on specific positions from a BAM file (in R)

Let's assume I have a BAM file and several positions that I would like to examine more closely in this alignment. My goal is to find out whether these positions are on the same reads and which ...
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32 views

Snakemake rule issue with bcftools view filtering

I am creating a bioinformatics pipeline using Snakemake doing everying from adapter trimming of raw sequencing data in .fq to mapping, SNP calling and SNP filtering. The issue i am having is when i ...
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A unified database for CNV, SNP, Indel and MSI

I am looking for a database or different databases where I can find information on different gene variants for a gene. As an example if I enter PPARG, I could be able to see SNPs, CNV, InDels and MSI. ...
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29 views

Output of allelic association doesn't write the rsID

I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the rsID (SNP), it just writes a dot. Output: ...
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29 views

Is there a way to calculate the Ka/Ks value in R/unix?

I am investigating the rate of synonymous non synonymous substitutions and would like to find the Ka/Ks value also known as dn and ds between multiple alleles? I want to investigate multiple alleles ...
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36 views

How do I remove allele annotations from SNP Ids in .bim file?

Hello every one i need help in editting my .bim file. So my .bim file looked like following. I want to convert the ids with chromosomal position from chr1_867635_C_T...
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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. ...
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Is SNPRelate the goto package for PCA of SNP data in R?

I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend? Many thanks,
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46 views

How to estimate the phenotypic variation explained by top SNPs from a GWAS study?

I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
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27 views

Biological datasets for polythetic classification

Question: What are some instances of polythetic datasets in biology? In particular, I am looking for a dataset to benchmark a machine learning algorithm optimized via episodic training. On polythetic ...
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54 views

How to make CIRCOS plot of VCF file?

I have 3 VCF files, I want to make CIRCOS plot just like the following: https://www.nature.com/articles/s41598-020-70527-8/figures/4 I try to follow the tutorial but could not understand. The genome ...
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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: ...
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How to plot a graph of Linkage disequilibrium with limited information

I have a snp information in an excel file and I used SNPstat to do some analysis. But I also need a plot of LD for these snps. But my file is not formatted as the most programs required (.ped, hapmap, ...
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42 views

How to know the number of SNP in my samples after running the population module in stacks

I am new to stacks for analyzing RAD-Seq data, I have run all the modules. I will like to know to get the total SNP from my sample after running the population module. Is there a command line to use ...
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32 views

Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
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50 views

Converting FASTA Sequences to SNP FASTA Format

I have two FASTA sequences. Each is from a different species' mitochondrial genome. The sequences are pasted below. ...
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35 views

Question about public availability of human SNP dataset with country of origin

Is there a publicly available data set for humans SNPs, preferably together with the country of origin? If so, could someone please point me towards it. I've looked through other questions on the site ...
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Denovo, Stacks: Getting an “ambiguous redirect” error

I tried running the following command ...
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65 views

Supplementary aligments in VAF

This question has also been asked on Biostars I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot. In my case I have some ...
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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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48 views

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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211 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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19 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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35 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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55 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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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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39 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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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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31 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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44 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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38 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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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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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 ...
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55 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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43 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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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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239 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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31 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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36 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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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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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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42 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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56 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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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
138 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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124 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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55 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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58 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 ...