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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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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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1answer
25 views

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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30 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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1answer
56 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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2answers
34 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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35 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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1answer
56 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
65 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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1answer
30 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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80 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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37 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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1answer
56 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
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2answers
48 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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78 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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1answer
61 views

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. ...
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1answer
73 views

How to download SNP data from specific regions, population and positions?

I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems. To do that, I've read a lot of papers and books in order to understand the main ...
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1answer
55 views

how to do analysis of a table content SNP?

I have a table with information about SNPs, the table has a total of 55127 rows. How can I know the number of gene mutations in the table and if a gene is present? The table is in xls format.
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verifybamid results with freemix < 2% and chipmix > 10%

I ran verifyBAMID on each 200 chip-seq BAM files with input merged vcf file of Genotypes of 600 samples ( 200 of them are chip-seq individuals). I had AF,AC,AN in the info column which was calculated ...
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1answer
125 views

update dbSNP ID

I have used dbSNP build 138 to tag 'rs' ID in my VCF file. But later I came to know that now dbSNP build 150 has been released. I want to update the rs IDs in my VCF file. I tried but I found a ...
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Error filtering SNPs with Plink

Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
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1answer
23 views

Human SNP databases other than dbSNP

I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm ...
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1answer
80 views

Generate SNP/indel annotation in Arabidopsis

I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. ...
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2answers
121 views

PCA on genotype matrix with multiple alleles

Consider an m x n genotype matrix of m haploid samples and n SNPs where each value is an allele encoded by an integer (0,1,2,3). Is there a good/standard way to encode the alleles in order to ...
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1answer
62 views

SNP data Download Help

I am new to the field of Bioinformatics. Single Nucleotide Polymorphism or SNP data are available on the the Internet to download.SNP related data are valuable for variety of reasons ranging from ...
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1answer
143 views

Is it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?

I have estimated genome-wide heterozygosity levels using maximum likelihood and classical substitution model implemented in package atlas. These estimates are way more robust than classical SNP ...
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1answer
90 views

Can I export the SNPs between whole genome alignments using the command line?

I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format: ...
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43 views

Post ipyrad filtering of SNP loci from GBS, based on SNP quality

I want to use SNPs produced by ipyrad analysis of GBS data in RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic relationships with about 40 congeners. An initial ...
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1answer
35 views

Assuming that we have the following SNP and phenotype data, is the SNP significantly associated with the phenotype?

So if I attempt this question using their method I put the data of genotype and phenotype into a data frame in R then use lm() to do linear regression and ...
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1answer
35 views

SNP located within a promoter region (pig)

I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip (WG-410). I want to know if these SNP are located within a ...
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1answer
34 views

remaining human genome variation that hasn't been sequenced?

Given all the genome variation information we have accumulated from resequencing human genomes up until now (early 2018), how much variation is left that hasn't been sequenced? EDIT: given one of the ...
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1answer
77 views

How to retrieve SNPs data of different humans?

How can I retrieve only SNPs from the dbSNP's FTP site. The files are gzipped and organized by human chromosome (i.e, chr[1-22,X,Y]), are these for one human? I need only SNPs data for various humans.
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2answers
57 views

Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?

I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
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1answer
94 views

Where can I find a list of SNP rs IDs that belong to the X chromosome?

Where can I find a list of SNP rs IDs that belong to the X chromosome? I'm trying to exclude the SNPs on X-chromosome in a data set, but I don't know where these SNPs come from. I tried to use ...
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how to plot LD between SNPs and CNVs

I have a bunch of CNVs which I have estimated LD between each allele of CNV with all SNPs across the entire human genome. I used my R-script to do a pairwise LD analysis. The following is the first ...
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2answers
63 views

Show presence of known mutation in RNA-seq data

We have RNA-seq fastq data from control (WT) patients and a patient with a point mutation at a known location in one gene. I'd like to retrieve the reads aligning to that gene and show the presence of ...
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3answers
245 views

Convert rs ID of one hg build to rs IDs of another build

I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping ...
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1answer
390 views

LD analysis in PLINK based on reference and a SNP list

I'm new to PLINK and genetics, and getting confused with two PLINK commands for LD analysis: plink --bfile hapmap --r2 --ld-window-r2 --ld-snp-list --ld-window <...
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2answers
53 views

Identifying relevant SNPs from a list

I have a list of all SNPs (a list of RsIDs) that fall in the coding sequence of several thousand human genes, and I'm looking for a convenient method to come up with a list of known SNPs that alter an ...
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1answer
612 views

Using PLINK to find SNPs in LD (Linkage Disequilibrium) with another set of SNPs

I have a list of SNPs (index SNPs). As my tagging SNPs, I want to use SNP data from here. The data has the following column headers: Chromosome, Position, MarkerName, Effect_allele, ...
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2answers
268 views

PLINK clump behavior on missing SNPs?

I have a long list of autoimmune-associated SNPs, and I want to boil it down so that I get one SNP representing each LD block. I chose to use PLINK's --clump option for this. I'm roughly following ...
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91 views

IGV jump to rsID location

Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box? For human and ...
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2answers
78 views

Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads

This question is slightly related to this one: Improve a reference genome with sequencing data Only in my case, I have a starting genome reference A, of a short phage genome, and reads from a related ...
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6answers
1k views

How to get a list of genes corresponding to the list of SNPs (rs ids)?

Is there a way for me to get a list of genes given a list of SNP rs ids? I found several questions asked with a similar goal years ago, and the answers are always about using multiple online tools, ...
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1answer
69 views

SNP-phenotype association analysis only using the SNPs on a specific gene

I know that the GWAS association p-value threshold is 1e-8. This makes sense because in GWAS, you make ~1 million hypothesis (i.e. use that many SNPs in the association test). However, let's say I do ...
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1answer
274 views

How to deal with correlated SNPs in GWAS?

I have population SNP data in VCF format, and I found that some SNPs have a great similarity across samples(> 99%). For example: ...
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1answer
70 views

What will be an appropriate mathematical distribution for SNP data?

I found that several papers describe SNPs as a binomial distribution with the probability of "success" equals to minor allele frequency. However, in my experiments, when I generate SNP array ...
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3answers
307 views

Is there any difference between SNPs 'AG' and 'GA' in association analyses?

I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, ...
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2answers
107 views

Is there a way to quickly verify the presence of some SNPs in Fastq files?

Is there a tool that can scan fastq files without assembling them for a custom list of user defined snps?
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1answer
203 views

Tool or script to parse annotated VCF files

I've annotated VCF files using snpEff and looking for a tool or script to parse the VCF file and clean up the file to make it interpretable for a biologist.
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1answer
130 views

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

Let's say I have the genome hg19 loaded into R via BSGenome ...