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Extract gnomad AF for specific position and REF/ALT allele with R

R allele frequency gnomad af annotation written 18 months ago by Nicolas Rosewick ♦ 9.0k

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262

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Problem with allele frequency calculation in vcf

vcf allele frequency written 11 months ago by BAGeno • 170

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1.6k

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Allele Frequency Thershold

1000g allele frequency annovar written 4.3 years ago by 786 • 50 • updated 8 months ago by Biostar ♦♦ 20

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216

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How to calculate the p-value of frequency of my study and control of some variants?

p-value allele frequency snp written 11 months ago by mullin.yu • 0

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264

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Plink allele with frequency greater than 0.05

allele frequency genomic plink genotype written 10 months ago by dishasharma35 • 0 • updated 10 months ago by genomax ♦ 90k

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358

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Require Genotypes In Vcf File In Order To Output Frequency Statistics

vcf allele frequency vcftools af written 9 months ago by ja4123 • 0

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190

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Allele frequency comparison between pairs of populations

software error allele frequency next-gen snp written 8 months ago by jaafari.omid • 50

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150

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Best way to get Allele Frequency in dbSNP file of SNPs in a different VCF file?

vcf allele frequency written 22 days ago by markgodek • 30

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Recent Replies

C: Help interpreting BLAST results? (Max score/Percent. Identity/E-values) by cia • 10
again,thank you very much!!
C: How do I subset VCF based on genotype? by Tine • 0
Thank you so much! What a nice and simple solution. I need to remember to check the bcftools docu...
A: How to download primary site data from TCGA? by Kevin Blighe ♦ 65k
It is possible to distinguish malignant / benign from the TCGA barcode ( https://www.biostars.org...
C: DESeq2 analysis with high number of samples by Kevin Blighe ♦ 65k
You are posting this question prematurely, it seems. Please proceed with your experiment and then...
A: Does bedtools intersect output overlaps with isoforms? by Kevin Blighe ♦ 65k
You can control what is output - can you please check the options for `bedtools intersect`, speci...
C: VariantToTable not calling HET HOM etc by Kevin Blighe ♦ 65k
Can you confirm that you have first posted this on GATK Support Forum? That would be the better p...
A: Methods to interrogate RNA-seq by Kevin Blighe ♦ 65k
Perhaps you can obtain some insight from my answer, here: https://www.biostars.org/p/305532/ Kevin
C: how to interpret a CNV scatter plot by Amitm • 2.0k
No worries. To understand better the outcome in pat.C, I would recommend to look into the 'segmen...
A: How do I subset VCF based on genotype? by Kevin Blighe ♦ 65k
Hi, There are indeed different ways to do this, including via standard shell commands. However,...
C: Alignng RNAseq data for gene prediction by Kevin Blighe ♦ 65k
Trinotate, part of the broader Trinity workflow, performs functional annotation: https://github.c...
C: Clustered GO-term heatmap by rpolicastro • 1.7k
To make the plot you linked to, you start with a data.frame that has 3 columns: gene, sample, and...
C: Clustered GO-term heatmap by ccha97 • 20
Thank you for your answer, their formula interface/compareCluster is exactly the sort of function...

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