Biostar

9,614 results • Page 2 of 193

Hi! I'm doing my master thesis and i have allele frequecies of 21 STR loci for 15 different populations. But I don't know how to do the input file for arlequin to compute...be like this: [Profile] NbSamples=14 DataType=FREQUENCY GenotypicData=0 GameticPhase=0 …

frequency arlequin inputfile

updated 8.6 years ago • soraiiafng

Hi, I would like to calculate absolute allele frequency differences (delta) for each SNPs of two populations (using 1000 genomes vcf data). I could

population genetics

updated 10.8 years ago • meganathan.pr

Hello! I have a problem with reverse allele frequency in my GWAS. I compare the allele frequency of SNP from GWAS with reference allele frequency. My results after...synchronization allele: ![X - reference frequency; Y - GWAS frequency][1] So, I want to understand how I can detect such SNPs to remove them from the analysis

GWAS Allele Frequency

updated 4.8 years ago • panacotaforcota

From what I understood, [allele frequency spectrum][1] is everything that concerns the frequency of all of the alleles studied in a population. It can...be estimated with Tajima's D, theta, etc. But how is it different from the *joint* allele frequency spectrum? [1]: https://en.wikipedia.org/wiki/Allele_frequency_spectrum

allele population structure

updated 7.0 years ago • beausoleilmo

I tried to use Bcftools to calculate allele frequency by SNP variants after bowtie 2 alignment. bcftools mpilup --redo-BAQ --min-BQ 30 --per-sample-mF --annotate...multiallelic-caller --variants0only -0v > new.vcf And after `+fill-tags` for AF, I used query to calculate AF for me. However, all position show AF: 0.5? I am confused how to calculate SNP allele frequency estimation in …

SNP

updated 22 months ago • gwyneth0011

I have a VCF file, and I need to calculate allele frequency for each variant by using code/script, I have the values for AN and AC within the file

vcf variant genome gene perl

updated 4.7 years ago • Nyksubuz

They describe that chart like that: > For each SNP, this effect is determined by how many effect alleles you possess (0, 1, or 2), the effect size of the SNP, and the frequency of the effect allele in your ancestry group. Each bar...Catalog and added my genotype from raw dna file. I put it in a table: SNP My Genotype Effect Allele P-value RAF Beta CI rs490647 AG A 3 x 10-7 0.246…

SNP effect size

updated 5.9 years ago • BobN

How can we calculate a risk allele population frequency of snps from 1000 genome browser

1000 genome browser snps risk allele frequency

updated 9.1 years ago • 12021560-040

the variant allele frequency(VAF) related to time-series, e.g. higher VAF related to early mutation, lower VAF related late occurred mutation...if the copy number amplification with late occurred mutation, this VAF might high if mutation allele- amplified or low if wild-type allele amplified. is there any tools to handling this kind of problem? to calculate corrected

sequencing SNP

updated 4.7 years ago • 9521ljh

Hi everyone, I have a list of 7000 SNPs referring to the hg19, and I was looking for the allele frequencies. Where can I find them? Usually I use the website gnomad to find the frequencies but I can't do this job for...SNP one by one. Any suggestion? furthermore, I've noticed that in different website for the same allele it is usual to find different values of frequency, how Is this possible? …

snp allele frequencies variants vcf

updated 3.1 years ago • Giulia.cosenza

Let’s say I have 10 known SNPs and I want to calculate what percentage of the population has all 10 of the risk alleles associated with these SNPs. Anybody know of any...tools are calculations for this? Furthermore, how could I go about finding the population frequencies of the 10, and then removing 1, finding

SNPs

updated 2.9 years ago • gtasource

really appreciate your help. i used bcftools to fill the tags for a vcf file and extract the allele frequency. for some positions I get two allele frequencies comma separated. what does it mean

allele position BCFTOOLS

updated 4.0 years ago • raalsuwaidi

How could I convert the Effect Allele Frequency (EAF) to Minor Allele Frequency (MAF) in GWAS summary statistics

gwas maf genomics genome-wide genetics

updated 5.2 years ago • bigfoot

Hi, I have a general query on various allele frequency terms usage while defining rare and common variants (both SNVs and SVs (structural variants). I have seen papers...where people have used population alternate allele frequency (AF) thresholds to define rare and common variants (for example gnomad and gnomad-SV). Many papers also use minor...allele frequency (MAF) threshold to define rare a…

rare common SNV SV VCF

updated 2.5 years ago • prasundutta87

I am new to genomics, and have a question about what allele frequency in a vcf exactly refers to. I have a bam file that represents sequencing done on one patient, and I want to understand...i.e. if the reference is A, and the SNP is G, are 40% of the reads calling G, or 90%) is this what allele frequency is describing? Or is it saying that in a population, if the allele frequency is .1, 10% of t…

vcf bam allele-frequency

updated 22 months ago • af15d938

I wanted to first try and calculate allele frequencies, and then from there calculate allele frequencies based on populations and so on. However, I...ran into an issue where while I was using plink, I would utilize the --vcf command to try and calculate frequencies. The frequencies were calculated, but the SNP names were missing. I used the following command in Git...tried to convert the file to …

snp frequencies vcf allele plink

updated 2.3 years ago • Shreyas

I have a question regarding the kits used for sequencing. I'm in a process of calculating the allele frequency of a group of samples, I have the VCF files however it was produced using different versions such as Agilent...SureSelect Human All Exon V4 , V5 and V6. My question is, for calculating the AF, can I do my calculations with all files regardless of the version? or I should separate them? …

Agilent SureSelect allele frequency version

updated 2.7 years ago • m.bamajboor

Center (30x on GRCh38). The VCF obviously provides overall and superpopulation-specific alternative allele frequency. A small proportion of alternative allele frequencies are not the minor allele with values such as 0.8/0.9...For example when I print %CHROM %POS %INFO/AF_EUR I can see this SNP, where the alternative allele frequency is clearly the major allele. (The VCF has already been filtered …

1000genomes vcf annotation

updated 2.5 years ago • Isobel

a few relevant lines from the actual file: ##INFO= <id=ac,number=a,type=integer,description="allele allele,="" alt="" as="" count="" each="" for="" genotypes,="" in="" listed"="" order="" same="" the=""> ##INFO=<id=af,number=a,type=float,description="allele allele...alt="" as="" each="" for="" frequency,="" in="" listed"="" order="" same="" the=""> ##INFO=<id=an,num…

frequency allele VCF

updated 2.3 years ago • Emoji

I have downloaded GnomAD vcf file and want to calculate the minor allele frequency of each variant in that file. But I am not quite sure how to do that. I have an INFO column...which has AC,AF, AN in there. Does AF refers to minor allele frequency for that variant? If not then how can I calculate the minor allele frequency. I've given below three variants

gnomAD genome

updated 4.4 years ago • Jamie Watson

GT:AD:DP 0/1:19,21:40 0/0:42,0:42 I am under the impression that to calculate the **minor** allele frequency (AF), I need to divide AD by DP. I need clarification for this specific calculation since...has two comma-separated values. Are the two comma-seperated values indicating the major and minor alleles? Does that mean for the calculation of the **minor** AF that I only care about th…

vcf minor allele frequency cancer

updated 5.8 years ago • cookersjs

Is there a way to find the allele frequency of gnomAD db with the rsID of my SNP data using gnomAD db in Python or R? If there is a specific rsID, I want to get...the total allele frequency and east asian allele frequency of this rsID from gnomAD db. I tried using the gnomAD_DB package in python...but there were many cases where the allele frequency could not be obtained. I think this part …

R python gnomAD

updated 21 months ago • sooni

VCF files from exome sequencing, merged all sites and converted to a bed file. Then, I calculated b allele frequency at every site in this cumulative bed file for every sample and prepared a per-sample input file with corresponding...Log R Ratios derived from a prior SCNA analysis. The above program calculates allelic imbalance by performing segmentation using input B Allele Frequency or rather…

sequencing next-gen snp SCNA BAFsegmentation

updated 8.1 years ago • stachele

I am fairly new to this field，and right now I am working with variant allele frequency for cancer genome,data is from cbioportal. I have read several articles and they claim mutant allele frequency...used to estimate the intra tumor heterogeneity by looking at the number of cluster of those variant allele frequency, this is the part I am not understanding since those variant allele frequency is…

genome gene

updated 5.5 years ago • 18982289189

wanted to say that I have analyze my NGS data and now I have a sheet of my variants along with their Allele frequencies in each of my sample (from VCF and Bam files). I wanted to ask what threshold of Allele frequency should I set...to pick my good quality variants? e.g. some people say that if Allele frequency in VCF file is more than 20% in VCF file it means your Variant is of good quality. Al…

NGS Variant VCF

updated 2.1 years ago • Maryam

22_20000722_G_A_b38", "22_20001035_C_T_b38"), class = "data.frame")][1] I want to calculate minor allele frequency for each snp(eg: 22_20000222_C_T_b38 ) across the samples. So basically for this SNP: 22_20000222_C_T_b38...I want to calculate its maf across all the 205 samples. Is there any way or formula to do it. Thank you. [1]: /media/images/cec2a316-07f5-4aa5

maf snp genotype

updated 2.1 years ago • rheab1230

do not know how we can distinguish between somatic and germline mutations by comparing their variant frequencies. I'm also a bit confused what is the difference and how we calculate the following: MAF (minor allele frequency) and...variant frequency. from NGS data, I have several tsv files that contains thousands of lines that contains minor allele, somatic and...grmline frequencies, each file f…

variation

updated 11.7 years ago • lo.hope81

I have a vcf file with SNPs called using the Torrent Variant Caller and I want to calculate their Variant Allele Frequencies. The issue is that there is both a DP (depth) and a FPD (flow depth) fields as well as...an AO (Alternate Allele Observations) and a FAO (Flow Alternate Allele Observations) fields and the two often disagree by a lot. Which pair should

snp sequencing vaf Ion-Torrent

updated 2.7 years ago • stamakro

Hi there, Could anyone show me a straightforward method to retrieve genotypic frequencies from a tped or vcf? I mean, not the expected frequencies calculated assuming Hardy Weinberg equilibrium from...the allelic frequencies, but the real genotypic frequencies. I found a way using plink's --hardy option, which gives you the genotype...counts, amongst many other stuff, and from these counts ret…

genotype vcf plink

updated 11.8 years ago • Peixe

I find set of SNPs that in 4 different population have same minor allele frequency and also same alleles. but I find that most of my alternative alleles are the alleles with major frequency

gene genome genetics

updated 2.7 years ago • star

Hello All, Where can i find allele frequency cut offs (or upper and lower range) for all the genes (for all the types of variants) to call variants polymorphic

frequency gnomAD gene allele

updated 3.6 years ago • luffy

Hi, Recently I ran MiSeq, but could you tell me what the difference between allele frequency and allele fraction is? Thank you

NGS MiSeq

updated 2.8 years ago • maricom

Hi all, I would like to ask how to calculate heterozygosity from 1000 genomes data. In the ENCODE study, one of the diversity index shown in [Figure 1][1] was calculated...The authors were written that "Heterozygosity was calculated basewise as 2pq, where p and q are allele frequencies estimated from the pilot sample of the 1000 Genomes YRI population". However, in the sample of 1000 genome...0…

snp genome

updated 2.8 years ago • suimye

I computed allele frequencies for a list of SNPs for a set of individuals in PLINK using the following line: ./plink --bfile Pop_Imputed_filtered...keep Pop.txt --freq --make-bed --out Pop Now, I want to compute allele frequencies for the same set of SNPs but for each individual, so it should calculate individual frequencies instead...contained in the Pop.txt file. I know that the out…

plink frequencies allele

updated 3.1 years ago • pifferdavide

Imagine 10 alleles (A-J), each with a 10% population frequency at one locus. 1. If you know that your sibling had alleles A,B, what are the probabilities...of observing any allele at your position in the pedigree. 2. If your nephew (on your mother's side) has alleles C,D what are the probabilities of observing...any allele at your position in the pedigree. 3. If your nephew (on your mother's sid…

frequencies IBD pedigrees allele

updated 2.7 years ago • literature.02

Hello! In the output from vcftools '--freq' option, you could get for example: CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} 1 861276 2 698 A:1 G:0 1 861292 2 698 C:1 G:0 1 861298 2 698 G:1 A:0 1 861315 2 698 G:1 A:0 It looks wonky because of single tab delimiters...the output from vcftools '--freq' option, you could get for example: CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} …

vcf vcftools MAF allele frequency allele

updated 7.6 years ago • Joel Wallenius

Hi all, I have a doubt regarding the ExAC database about the allele frequency. For some variants the allele frequency is over 50 %. How to interpret it. Does it mean that it is more frequent

exac

updated 8.5 years ago • kiruphagaran

Hello all , I'd like to understand of Allele frequency. If I change allele frequency threshold from 0.2 to 0.02, Color graph of bases are appear (from gray color) Does

IGV alignment bam

updated 8.2 years ago • clear.choi

Hi all, I am looking to calculate the frequencies of all possible combinations of a group of SNP genotypes, in a population. This would be done based...on the minor allele frequencies acquired in our population data. I just have a question on whether the following is the right way to do it...If for example, we have three SNPs, their alleles, and their minor allele frequencies, with A2 being the…

genotype frequency allele

updated 6.6 years ago • Volka

It is easy to get allele frequency for a site (mutation/snp etc.) from a bam file. How do we get the allele frequency of a gene (in some metric) from a...bam file, like dominant allele frequency of a gene, for instance? Any advice from population genetics people here? Thanks

allele frequency

updated 7.3 years ago • Kasthuri

Hi everyone, I am searching for a downloadable database of HLA allele frequencies by country (especially European countries). I have found a nice database here - this is the ideal example...bigger database http://www.allelefrequencies.net, but I was not able to automatically download the allele frequencies which makes the work very slow. Do you know a good HLA allele frequency database per c…

genome snp gene

updated 5.0 years ago • levshagam

the ClinVar database (Baker, 2012) from likely benign Exome Sequencing Project (ESP; Fu et al., 2013) alleles with a derived allele frequency (DAF) ≥5% (Fig. 1b, n = 10 000 pathogenic/10 000 likely benign). I have downloaded ESP variant...following link: [Link to ESP vcf file][2] And info column of these vcf files does not have derived allele frequency. It has minor allele frequency. So my que…

allele-frequency variants vcf genome ESP

updated 3.8 years ago • peter

Hello, I want to estimate allele frequency at different read depth (10X, 20X, 30X, and so on). I have variants call output in vcf format. I also estimated read...10X, 20X etc. I am not sure if this is a correct way to proceed. Is there any better way to estimate allele frequency at different depths? Any suggestion will be appreciated. Thanks

allele depth frequency vcf read

updated 3.9 years ago • rthapa

Guys, I am running GATK on bam file for variant calling. In the output file, I noticed that the Allele frequency is computed as 0.5 and 1.00. What may be the reason for this? Is it calculated correctly

VCF Allele GATK frequency

updated 3.5 years ago • shivangi.agarwal800

and Affymetrix). Does anyone know if sometimes the softwares have "problems" to assign the B-allele frequency correctly? I know that sometimes they recenter the logR, but it doesn't happen with B-allele frequency, right

snp

updated 6.0 years ago • beaferbl

Can we adjust variant allele frequency in any of the tools like VarScan2, Mutect etc

next-gen sequencing

updated 6.1 years ago • sruthi

I got a VCF which I need to calculate variant allele frequency for each variant at each position. My understanding is that variant allele frequency...mates="" mq="255" or="" read="" with=""> ##INFO=<id=ad,number=1,type=integer,description="allelic alleles="" alt="" and="" depths="" for="" in="" listed"="" order="" ref="" the=""> ##FORMAT=<id=gt,number=1,type=string,description="geno…

vcf allele-frequency

updated 2.0 years ago • jason

Hi all, Following Lars question, is there a way to calculate the population specific allele frequencies from the 20101123 1000 genome release using tabix and vcftools? Currently...I am just able to extract the genotypes with tabix for defined chromosomal regions and calculate their frequency with vcftools. However I know those frequencies are underestimated due to the mixture of populations

genome allele tabix vcftools population

updated 13.4 years ago • Noel

my plink binary files. That is, they have the same chromosome and position, but different alternate alleles. Using plink, I would like to keep only that with the highest alternate allele frequency for each identical chromosome...is `'force-first'` which would only work if the SNPs were already ordered by alternate allele frequency and I'm not sure how to do this or if it's possible. I also thou…

QC plink

updated 4.0 years ago • rem

paired ended). The resulting alignments look noisy. Since we are trying to fish for very low frequency variants, is there any way to count for the noises? Like how to calculate error rate in MiSeq bam files and how to consider...them when calculating allele frequencies. Any input will be appreciated. Here is an example of the noise I am referring to

MiSeq low frequency variant calling

updated 10.6 years ago • Nikleotide

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