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3
votes
3
replies
5.5k
views
Merge two phased vcf files from 2 pops keeping same ref allele in merged file
bcftools beagle plink
updated 2.7 years ago by • 0 • written 5.1 years ago by ▴ 150
5
votes
7
replies
2.5k
views
Retrieve genomic physical coordinates of 3'UTR for set of genes
3'UTR
updated 2.7 years ago by ▴ 70 • written 3.8 years ago by ▴ 150
2
votes
1
reply
3.5k
views
Convertf. Convert from PED to EIGENSTRAT format
convertf
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by ▴ 150
0
votes
1
reply
412
views
Get % of identity of a list of human genes with their homologous genes in other species
alignment sequence
updated 3.2 years ago by 134k • written 3.2 years ago by ▴ 150
0
votes
0
replies
848
views
Phases switches in local ancestry inference (LAMP-LD vs RFMix)
LAMP-LD RFMix phasing phase switches
3.4 years ago by Mr Locuace ▴ 150
0
votes
0
replies
2.1k
views
Comment: C: Find genome coordinates of nucleotide sequence within specific gene
3.4 years ago by Mr Locuace ▴ 150
2
votes
2
replies
2.1k
views
Find genome coordinates of nucleotide sequence within specific gene
Biopython FASTA Physical positions
updated 3.4 years ago by 35k • written 3.4 years ago by ▴ 150
0
votes
0
replies
2.5k
views
Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
3.8 years ago by Mr Locuace ▴ 150
0
votes
1
reply
2.5k
views
Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
3.8 years ago by Mr Locuace ▴ 150
0
votes
1
reply
824
views
Find gene affected by specific regulatory region
promoter regulation SNP enhancer
3.8 years ago by Mr Locuace ▴ 150
1
vote
1
reply
2.4k
views
Batch query of ancestral and derived alleles from Ensembl
Ensembl SNP Batch ancestral-allele
updated 14 months ago by 40k • written 7.7 years ago by ▴ 150
0
votes
0
replies
1.7k
views
Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
4.1 years ago by Mr Locuace ▴ 150
0
votes
1
reply
1.7k
views
Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
4.1 years ago by Mr Locuace ▴ 150
3
votes
4
replies
1.7k
views
ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.gz X_2.fastq.gz
fastq paired-end single-end ENA
updated 4.1 years ago by 26k • written 4.1 years ago by ▴ 150
0
votes
0
replies
1.1k
views
Convert from plink or vcf to bgl format
vcf bgl plink
4.2 years ago by Mr Locuace ▴ 150
3
votes
1
reply
1.4k
views
Convert physical positions from Hg18 to Hg19
liftover
updated 4.3 years ago by 76k • written 4.3 years ago by ▴ 150
0
votes
0
replies
1.1k
views
Phasing genotype likelihood data and merging them with phased genotype calls data.
phasing genotype likelihood genotype calls
4.4 years ago by Mr Locuace ▴ 150
2
votes
1
reply
1.6k
views
Plink2. psam file missing in 1000G Phase3
plink2
updated 4.6 years ago by 10k • written 4.6 years ago by ▴ 150
0
votes
1
reply
39k
views
Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
4.6 years ago by Mr Locuace ▴ 150
8
votes
2
replies
2.2k
views
Get all SNPs that are in high linkage disequilibrium (based on D') for a set of SNPs
plink SNP LD
updated 4.7 years ago by 10k • written 4.7 years ago by ▴ 150
0
votes
0
replies
7.1k
views
Answer: A: How to calculate Hudson's Fst at Population and SNP level?
4.9 years ago by Mr Locuace ▴ 150
0
votes
0
replies
3.4k
views
Comment: A: Converting ms or msms output to PLINK or VCF files
4.9 years ago by Mr Locuace ▴ 150
0
votes
0
replies
1.2k
views
LD pruning before or after phasing for calculating site frequency spectrum?
SNP LD
5.0 years ago by Mr Locuace ▴ 150
0
votes
0
replies
5.5k
views
Comment: C: Merge two phased vcf files from 2 pops keeping same ref allele in merged file
5.1 years ago by Mr Locuace ▴ 150
6
votes
4
replies
4.9k
views
VCFtools. Get rid of DS:GP phased genotypes while keeping GT and remaining fields
VCFtools
5.1 years ago by Mr Locuace ▴ 150
0
votes
0
replies
953
views
Run Husdon's ms with ABCtoolbox2.0
ABC ABCtoolbox Hudson ms
5.3 years ago by Mr Locuace ▴ 150
0
votes
0
replies
2.4k
views
Comment: C: Convert list of rs IDs from one format to another
5.4 years ago by Mr Locuace ▴ 150
3
votes
5
replies
2.4k
views
Convert list of rs IDs from one format to another
SNP identifiers eQTL GTEx
updated 5.4 years ago by 16k • written 5.4 years ago by ▴ 150
0
votes
0
replies
2.4k
views
Comment: C: Convert list of rs IDs from one format to another
5.4 years ago by Mr Locuace ▴ 150
0
votes
0
replies
2.3k
views
Comment: C: Get genomic coordinates for protein domain
5.4 years ago by Mr Locuace ▴ 150
0
votes
1
reply
2.3k
views
Comment: C: Get genomic coordinates for protein domain
5.5 years ago by Mr Locuace ▴ 150
3
votes
6
replies
2.3k
views
Get genomic coordinates for protein domain
protein domain coordinate
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 150
0
votes
0
replies
2.1k
views
Comment: C: Reference & alternative alleles extracted from 1000G, Phase 3
5.6 years ago by Mr Locuace ▴ 150
3
votes
0
replies
2.1k
views
Answer: A: Reference & alternative alleles extracted from 1000G, Phase 3
5.6 years ago by Mr Locuace ▴ 150
4
votes
5
replies
2.1k
views
Reference & alternative alleles extracted from 1000G, Phase 3
vcf 1000G ref allele
5.6 years ago by Mr Locuace ▴ 150
0
votes
0
replies
2.1k
views
Comment: C: Reference & alternative alleles extracted from 1000G, Phase 3
5.6 years ago by Mr Locuace ▴ 150
0
votes
0
replies
1.8k
views
Comment: C: Where to download official reference and alternative alleles from 1000 Genomes?
5.6 years ago by Mr Locuace ▴ 150
0
votes
1
reply
1.8k
views
Comment: C: Where to download official reference and alternative alleles from 1000 Genomes?
5.6 years ago by Mr Locuace ▴ 150
2
votes
6
replies
1.8k
views
Where to download official reference and alternative alleles from 1000 Genomes?
1000 Genomes reference allele Plink
updated 5.6 years ago by 10k • written 5.6 years ago by ▴ 150
0
votes
0
replies
1.2k
views
How to calculate the effective population size of part of a recently admixed genome?
effective population size SNP
5.7 years ago by Mr Locuace ▴ 150
0
votes
2
replies
7.6k
views
Comment: C: Convert vcf files with phased genotypes to standard haplotype format
5.7 years ago by Mr Locuace ▴ 150
8
votes
5
replies
7.6k
views
Convert vcf files with phased genotypes to standard haplotype format
haplotype vcf .hap
written 5.7 years ago by ▴ 150
0
votes
0
replies
2.0k
views
Comment: C: Plink. Convert ped files of artificially mixed population into vcf using recode
5.7 years ago by Mr Locuace ▴ 150
1
vote
2
replies
2.0k
views
Plink. Convert ped files of artificially mixed population into vcf using recode
Plink vcf phasing
updated 5.7 years ago by ▴ 230 • written 5.7 years ago by ▴ 150
3
votes
1
reply
2.1k
views
Plink. How to create small .ped file from big .ped file?
plink
updated 5.8 years ago by 10k • written 5.8 years ago by ▴ 150
1
vote
1
reply
3.8k
views
Comment: C: Why removing SNPs with MAF<5% for Fst calculation?
5.9 years ago by Mr Locuace ▴ 150
4
votes
7
replies
3.8k
views
Why removing SNPs with MAF<5% for Fst calculation?
snp maf Fst
updated 5.9 years ago by 86k • written 5.9 years ago by ▴ 150
1
vote
0
replies
4.7k
views
Comment: C: Using Plink, get allele frequencies for a subset of individuals
6.0 years ago by Mr Locuace ▴ 150
0
votes
1
reply
4.7k
views
Comment: C: Using Plink, get allele frequencies for a subset of individuals
6.0 years ago by Mr Locuace ▴ 150
3
votes
12
replies
4.7k
views
Using Plink, get allele frequencies for a subset of individuals
Plink Subset individuals
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by ▴ 150
66 results • Page 1 of 2
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