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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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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3 votes
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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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VCF file inspector app with GUI

Does anyone know a good, free-to-use VCF file inspector app (Mac OS, with GUI) where I can browse the content of a VCF file similarly to bamseek*? I would like to browse SNP annotation split by ...
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How to split genotypes into two groups from a SNP txt file contains -1, 0 and 1 in R?

I have a SNP file(it is 96 obs. of 1178 variables with -1, 1 and 0 and in some places NA) and I need to calculate Jaccard genetic distance from them in R. Is there any way to convert these 3 values to ...
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HG19 Position meaning

I am looking at genomic data (HG19). I have many SNPs, their chromosomes and positions. I want to look at certain SNP (suppose its chromosome is 1 and position 77,226,919), and extract all SNPs in ...
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Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?

I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is... I have a VCF/PLINK format file of ~8,000 individuals ...
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What to use to determine SNPs in a population? How to find significant SNP variation between generations?

I have a population in the hundreds and did an Illumina pool-seq (ended up with ~100bp reads for the whole population). I have the reference genome for the species and now need to align all the ...
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Combine all alternate alleles

I have a vcf with multi-allelic SNPs, e.g. REF: A and ALT: G, C. I would like to combine all reference alleles to the most ...
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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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1 answer
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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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1 vote
1 answer
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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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1 answer
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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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1 vote
2 answers
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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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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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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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3 votes
1 answer
104 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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1 answer
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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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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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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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1 answer
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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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1 answer
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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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1 answer
92 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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1 answer
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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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-1 votes
2 answers
105 views

Denovo, Stacks: Getting an “ambiguous redirect” error

I tried running the following command ...
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1 answer
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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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567 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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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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0 votes
1 answer
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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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1 vote
1 answer
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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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1 vote
1 answer
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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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1 vote
1 answer
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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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1 vote
2 answers
43 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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1 answer
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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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1 vote
1 answer
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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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2 votes
1 answer
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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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1 vote
0 answers
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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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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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