Biostar

9,603 results • Page 1 of 193

Hi I'm using **1000 genome browser** and want to retrieve data related to Allele frequency using Allele Frequency Calculator. When I entered chromosome and gene position and after selecting population...Mapping file and Chromosomal region. Now what should I do or anyone can guide me that how to use Allele Frequency Calculator plz

1000 genome browser Allele Frequency Calculator

updated 9.0 years ago • 786

Hi everyone I need to understand Minor allele frequency A SNP with a allele (G) frequency of 0.40 implies that 40% of a population has G allele versus the most common...allele (major allele), which is found in 60% of the population. If a SNP allele frequency is 0.05 how will be calculate its percentage...in the population Please explain with calculation Regards

SNP next-gen

updated 3.2 years ago • Tark

related and unrelated individuals. I have done the joint genotype calling and calculated the allele frequency using VCFtools. But as its a mixed population what is the ideal way to calculate allele frequency?. I would...like to make an in-house variant database from our available exomes and the corresponding allele frequencies will be used to filter the variants. It would be helpful if you can g…

Allele frequency Joint genotype calling

updated 8.1 years ago • nkausthu

Hello, I have VCF files and would like to calculate LD r^2 values from allele frequencies since my data is not phased. VCFTools doesn't seem to be working, it is reporting

r2 vcf

updated 10.8 years ago • Adrian Pelin

I have more than 800 snps with rs ids, i want to calculate the allele frequency of these snps in British (GBR) population from 1000 Genomes Project. The thing is that i can calculate...the allele frequencies of super population like European (EUR) using VEP script but unable to find the way to calculate the allele...frequency of specific population like British (GBR) population

vep allele frequency

updated 4.1 years ago • Abdul Rafay Khan

Hello, I have to calculate the b-allele frequency from a vcf file. But I have some problems to understand some genotypes. For example : 1/1:17:283...34,24:**2,15**:69,68 AD = 2,15 How can i calculate the BAF ? ( number of reads of the alternatif allele/ number of reads) I don't know if 17/17 (=1) it's correct or not ? And if the

vcf frequency

updated 8.1 years ago • Maj

Hi, I want to calculate B allele frequency from a vcf file. I found that vcftools can be used to estimate allele frequency of REF allele and...ALT allele. I wonder if vcftools could also estimate B allele frequency. Are there other tools that we could use for calculation

snp

updated 4.6 years ago • rthapa

I have a 23andMe GWAS summary statistics dataset. Herein, I have been given the frequency of allele A, the frequency of allele B, and Counts of AA, AB, BB genotypes in controls and cases. How can I calculate the

MAF GWAS PGS

updated 5 months ago • Priyatam

SNPs for 100 samples (divided into a dozen varieties), and I want to group them by variety and then calculate allele frequencies separately. The files are very large and cannot be easily split. Does anyone have any ideas, it...understood that each polyline represents a variety, and I can intuitively see the difference in SNP frequency between varieties）![enter image description here][1] [1…

frequency allele

updated 2.6 years ago • yoser4

Is it possible to calculate a population allele frequency for a novel variant? How

variant population Novel allele frequency

updated 2.7 years ago • erzal.scarlett3

with obtaining predictions from a dataset of tumor samples. One of the predictors we need is Variant Allele Frequency (VAF), so I downloaded one tumor dataset from the TCGA data portal to see how this calculation might be done...I understand what Variant Allele Frequency is in general, however I cannot seem to understand how the calculation is done in practice. The dataset has...What I wish is t…

genome R

updated 7.9 years ago • mp85

are the product of multiple different SV callers. While some of the approaches I use estimate the allele frequency for called breakpoints, others do not, so in some cases I have high quality variants that lack allele frequency...estimates. Because of this (and **), I would like to be able to calculate allele frequencies for a list of genomic coordinates. Allele frequencies in this context ref…

genome next-gen

updated 7.2 years ago • nanana

Hi, every one I have genotype dosage value between 0-2 and now I am interested to calculate Allele frequency through that. Any one has thoughts for that kindly let me know

SNP

updated 4.5 years ago • drsachinbioinfo

I want to use summary statistics containing only the Effect Allele Frequency (EAF) and not the Minor Allele Frequency (MAF) as base dataset for PRS calculation in PRSice2. It would be possible

gwas prs polygenic risk scores maf PRSice

updated 5.2 years ago • bigfoot

Does anyone know of a tool that can take MS coalescent simulator output format as input and calculate the mean absolute allele frequency different between two populations for the simulated loci? I've simulated 100...10kb regions of two divergent populations and would like to calculate the absolute allele frequency difference at each polymorphic site and then calculate the mean across the locus

ms simulations allele frequency

updated 7.1 years ago • Rubal

The 1000 Project released a tool that will calculate allele frequency by population in a single vcf file. There is a [web interface][1], and they recommend only querying...want to compare to your samples quickly. [1]: http://browser.1000genomes.org/Homo_sapiens/UserData/Allele

MAF allele-frequency vcf

updated 3.4 years ago • Katie D'Aco

Hello, I am wondering if there is a paper or a workflow which deals with individual-level allele frequencies. In plink so far I only see the option to calculate allele frequencies for all individuals (prior doing...Merge --max-maf 0.05 --exclude inversion.txt --range --indep-pairwise 50 5 0.2 --out indepSNP and calculate allele frequencies plink --bfile Merge --extract indepSNP.prune.in -…

allele frequencies clustering plink

updated 4.6 years ago • anamaria

Hello everyone, I use vcf tools to find AF values by using this command: vcftools --gzvcf $SUBSET_VCF --freq2 --out $OUT --max-alleles 2 The output I got from this is: chr pos nalleles nchr a1 a2 <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> 1 22 16050408 2 846 0.944 0.0556 2 22 16050612...find AF va…

AF VCF snp calc

updated 3.7 years ago • rheab1230

Dear all, I have 100 VCF files (100 different samples). I would like to calculate allele frequency in specific sites. In one specific locus I have three genotypes (GATK best practices workflow...30 samples (ref hom) A/G occurring in 21 samples (het) G/G occurring in 49 samples (alt hom) Frequency of genotype would be: A/A = 0.3 A/G = 0.21 G/G = 0.49 But how do I c…

genotyp vcf next-gen freq

updated 5.0 years ago • John

about the right way. My final aim is to convert z-scores to betas for my GWAS. I need the minor allele frequencies for my SNPs for the equation to convert z-scores to betas but I only have effect allele frequencies in my...GWAS. Wouldn't the minor allele frequency just be (Assuming biallelic SNPS): 1 - effectallelefreq if A1freq>0.5 and maf=eaf if eaf<0.5 Thank you

SNP gwas maf

updated 5.1 years ago • rk

Dear all, I am employing the Identification Test for 200 samples. But I don't know how to calculate the allele frequency as well as OH-observed heterozygosity, EH-expected heterozygosity, SE-standard error of EH

next-gen

updated 8.4 years ago • lengocthien

a vcf file generated from a few hundred samples. For each variant within the file, I would like to calculate the allele frequency of each allele and then add that information as a field into the 'INFO' field of the file. I know...that I can use vcftools to generate the allele frequencies, but I'm at a bit of a loss as to how I can add that back into the INFO section of the vcf. Alternatively, is …

allele vcf maf frequencies

updated 3.5 years ago • eric.londin

Hi everyone: I have a VCF file having multiple population samples. Is there any way to calculate the observed counts of genotypes called and observed genotype frequency of a subset of individuals from a given...freq) : 0|0 : 0.2, 0|1: 0.5, 1|1: 0.3 just an analogous to --freq option in VCFtools field that calculates the allele frequency of REF and ALT allelic forms at given site. Thanks a l…

ngs vcf

updated 7.0 years ago • SOHAIL

Hi I've been reading about how dbSNP stores allele frequencies of a SNP. I've looked at the schema and the handbook but I can't find information about how they calculate...frequency data many thanks

allele frequency

updated 14.0 years ago • Andrea_Bio

Hi, all What is gnomAD allele frequency? How to calculate the population allele frequency of a variant in gnomAD? What is the difference between

AF gnomAD

updated 4.0 years ago • Eric Wang

Hi all, I am trying to use SNPRelate R package for some analysis and I began calculating allele frequencies from plink data with the function snpgdsSNPRateFreq. However I didn't find any way to do these calculations

SNPRelate allelefrequencies plink SNP R

updated 4.0 years ago • irieljoerin

How to use allele frequency calculator of 1000 genome browser with external files? How can I prepare the vcf file of the snps to be used...in allele frequency calculator

allele frequency calculator external files

updated 9.0 years ago • 12021560-040

Hi all, So, I am interested in computing the VAF (variant allele frequency) by extracting values from a VCF file. From my understanding, the VAF is calculated as follows: AD(second entry...AD = 5,10 DP = 15 VAF = 10/15 Is this correct? However, I've seen that sometimes the frequency of the most frequent (or less frequent) allele is computed. Hence it would be 8/12 and 10/15 (or 4/12 …

sequencing

updated 6.2 years ago • JJ

HI, I have 500+ MAF files of exome sequencing. I want to get the allele frequency for all population in Exac. I have used awk script to match my variants in MAF files with the VCFs from EXac...database. However, Exac only provides the allele count and allele number (AC ; AN) for population specific and I need to calculate the frequency. Is there a tool or script...available to calculate the p…

EXac MAF sequencing

updated 8.2 years ago • jan

Can anyone explain how to calculate the allele frequency of an SNP marker with description: SNP 1 Row Mapping Format: "0" = Reference allele homozygote...1" = SNP allele homozygote, "2"= heterozygote and "-" = double null/null allele homozygote (absence of fragment with SNP in genomic representation...And I would be glad if someone explain how to calculate the minor and major allele frequencies a…

R next-gen genome snp sequencing

updated 5.4 years ago • albertoogy

several VCF files of individual haploid samples using GATK 4.1.7.0 and the variants have their allele frequencies as 1. I would like to calculate their empirical allele frequencies for subsequent plotting of their site...frequency spectrum. How do I go about this? Thanks in advance

allelle frequency VCF GATK Haploid

updated 4.7 years ago • drowl1

I am calculating allelic frequency for somatic variants. VEP gives a VCF file, for example that has: 9761707 G>A and outputs DP FDP SDP SUBDP...C DP FDP SDP SUBDP AU CU GU TU 153 0 0 0 0,0 77,79 0,0 76,76 How can I calculate the allele frequency from this information? I don't quite understand why in the first case there is nothing on AU...the first one an…

VEP variant

updated 10 months ago • ramiro.barrantes

Each genotype count is 250, 200, 40, 300, 120, and 90 respectively. I have been asked to calculate the allelic frequencies to determine LD and I am unable to. Any suggestions

SNP

updated 9.0 years ago • ojinjide

a VCF with multiple individuals from multiple populations and I would like to get a summary of the allele frequency spectrum for each population. I know that VCFtools has some nice options for outputting allele frequencies...However my data is from non-model organisms and I think using the reference/derived alleles for calculating allele frequencies is resulting in some serious biases. So I am l…

allele-frequency vcf pop-gen genome

updated 3.5 years ago • Rubal

Given genotype information (SNP allele frequencies) from different pooled populations, how can I calculate the probability (or significance, or some confidence...value) of the populations having different allele frequencies? I'm not terribly interested (and it's easy to do anyway) in estimating the actual allele frequencies, just...the probability of it differing. E.g. if I have alleles A and C…

snp statistics

updated 12.6 years ago • Ketil

Is there a way to force Plink to compute frequency with respect to a specific allele (NOT minnor allele frequency), for example using "--a2-allele" with a list of reference...alleles? plink -bfile --freq --extract list.snps --a2-allele list.reference.allele Thank you

frequency snp plink

updated 4.0 years ago • jamespower

Hello everyone, I'm learning how to analyze genome sequencing data and questions answered on these forums have been an immense help! Time to ask my own question: I've used BWA to align my sequences to a reference genome, then samtools mpileup to call variants, then shoremap to analyze the variants. I noticed that the allele frequencies of variants given by shoremap convert are much lower than …

shoremap allele-frequency

updated 23 months ago • emilywynn6

article: [article][1] In this article, authors mention and I quote **'pathogenic variants with allele frequencies greater than 0.01% were well characterized in publications and included many founder mutations.'** I want...to make if I understand allele frequency correct. Does allele frequency greater than 0.01% means variants for whom the alternative allele count...is greater than 1 so t…

snp allele frequency

updated 3.2 years ago • peter

How is allelle frequency calculated ? This a variation where Allelle Frequency (AF) is 0.500 and AD = 57,36 and DP = 93 My understanding...How is allelle frequency calculated ? This a variation where Allelle Frequency (AF) is 0.500 and AD = 57,36 and DP = 93 My understanding about AF calculation is `36 / 93 = 0.387096774` chr1 976215 rs7417106 A G 687.60 . AC=1;AF=0.500;AN=2;BaseQRankS…

vcf allelle frequency exome

updated 4.2 years ago • dare_devil

are only present in one patient. I think the high LOD for such variants might be due to the major alleles (the reference allele) that is present in most of the patients. This is problematic because reference allele should...not be considered as a variant. Here are my questions: 1. Why Merlin is using the major alleles and giving these high LODs? 2. Should we include the reference (major) alle…

pLINK Merlin Linkage

updated 3.3 years ago • Arton

how to find the allele frequency? is any online tool is there? allele frequency table for human. most commonly found allele in human

allele frequency

updated 12.2 years ago • anjanapaleri4

Biostars Leaders, Freebayes(version:v1.0.1-1-g683b3cc-dirty) defines AF as Description="Estimated allele frequency in the range (0,1]", but the values are always either 0.5 or 1.0, and they are not actual observed frequencies. I...have observed the same with GATK's HaplotypeCaller, and I have custom calculated the actual frequencies from Ref & Alt Alleles i.e. from the AD field. Freeba…

next-gen

updated 8.1 years ago • gsr9999

Hi I'm using Allele Frequency Calculator of 1000 Genome browser. I retrieved the allele frequency of 6:20534457-21232404 region from...it and obtained the following results. I just wanted to ask which frequency threshold I should select to call a snp associated with risk?? CHR POS ID REF ALT PJL_TOTAL_CNT PJL_ALT_CNT PJL_FRQ

allele frequency calculator 1000 genome browser

updated 8.9 years ago • 786

Good morning, I am looking for a way to calculate allele frequency for my dataset. I'd like to use the 1000 genome project files as reference panel. My file is structured...Good morning, I am looking for a way to calculate allele frequency for my dataset. I'd like to use the 1000 genome project files as reference panel. My file is structured in this way: SNP effect_allele other_allele b…

frequency allele

updated 3.2 years ago • salvatore.dantona

Hello, I am trying to calculate genome-wide FST pairwise values for every gene between all my isolates which I sequenced using NGS. I am offered...the default method using allele-frequencies coming from Hartl and Clark (2007), and the allele-counts method by Karlsson et al. (2007). Would anyone be able

NGS FST popgen

updated 3.5 years ago • Adrian Pelin

Hi All! I have sanger imputed genotype files and want to filter them based on MAF. Unfortunately they do not contain MAF scores. Is there an easy way to calculate MAF from this file? For reference here is an exmaple of what it does contain: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT...to filter them based on MAF. Unfortunately they do not contain MAF scores. Is t…

snp genome

updated 6.5 years ago • rshoobs

and millions of SNPs. The individuals can be divided in 15 to 25 populations. I would like to calculate the allele frequencies for each SNP on each population. Has someone got a R script doing this? Thank you

R SNP

updated 6.1 years ago • gwenola.tosser

Hello everyone! I'm looking for a tool that performs allele frequency calculations within the Galaxy Platform. I don't have much command line interface knowledge so I would avoid

galaxy allele-frequency

updated 19 months ago • LeandroF.

Could somebody please help me understand: What is the significance of Minor Allele Frequency? how Minor Allele Frequencies are used in GWAS in the selection of SNPs? What does Minor Allele Frequency...being zero signify beyond saying that the population is homozygous with dominant allele. Thanks for your time

allele frequency gwas

updated 14.1 years ago • Sashi Kiran Challa

Hello dears all, I am working on a whole genome data on a fish species. Now I want to calculate the allele frequency between pairs of populations and for this I tried to use the popoolation2. First the bam files...and then the protocol based on the website's guideline was proceed. But in the last step for the allele frequency calculation the command has been done incompletely. I thought it can be…

SNP next-gen Allele frequency software error

updated 5.3 years ago • jaafari.omid

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