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3
votes
4
replies
1.5k
views
Where can I get a list of SNPs mapping overlapping genes in humans?
SNPs
updated 21 months ago by 36k • written 21 months ago by ▴ 180
3
votes
3
replies
7.7k
views
Merge two phased vcf files from 2 pops keeping same ref allele in merged file
bcftools beagle plink
updated 4.7 years ago by • 0 • written 7.1 years ago by ▴ 180
5
votes
7
replies
4.5k
views
Retrieve genomic physical coordinates of 3'UTR for set of genes
3'UTR
updated 4.7 years ago by ▴ 70 • written 5.8 years ago by ▴ 180
2
votes
1
reply
4.9k
views
Convertf. Convert from PED to EIGENSTRAT format
convertf
updated 5.0 years ago by ▴ 20 • written 5.0 years ago by ▴ 180
0
votes
1
reply
685
views
Get % of identity of a list of human genes with their homologous genes in other species
alignment sequence
updated 5.2 years ago by 153k • written 5.2 years ago by ▴ 180
0
votes
0
replies
1.2k
views
Phases switches in local ancestry inference (LAMP-LD vs RFMix)
LAMP-LD RFMix phasing phase switches
5.4 years ago by Mr Locuace ▴ 180
0
votes
0
replies
3.4k
views
Comment: C: Find genome coordinates of nucleotide sequence within specific gene
5.4 years ago by Mr Locuace ▴ 180
2
votes
2
replies
3.4k
views
Find genome coordinates of nucleotide sequence within specific gene
Biopython FASTA Physical positions
updated 5.4 years ago by 36k • written 5.4 years ago by ▴ 180
0
votes
0
replies
4.5k
views
Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
5.8 years ago by Mr Locuace ▴ 180
0
votes
1
reply
4.5k
views
Comment: C: Retrieve genomic physical coordinates of 3'UTR for set of genes
5.8 years ago by Mr Locuace ▴ 180
0
votes
1
reply
1.2k
views
Find gene affected by specific regulatory region
promoter regulation SNP enhancer
5.8 years ago by Mr Locuace ▴ 180
1
vote
1
reply
2.9k
views
Batch query of ancestral and derived alleles from Ensembl
Ensembl SNP Batch ancestral-allele
updated 3.2 years ago by 45k • written 9.7 years ago by ▴ 180
0
votes
0
replies
2.6k
views
Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
6.1 years ago by Mr Locuace ▴ 180
0
votes
1
reply
2.6k
views
Comment: C: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
6.1 years ago by Mr Locuace ▴ 180
3
votes
4
replies
2.6k
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 6.1 years ago by 27k • written 6.1 years ago by ▴ 180
0
votes
0
replies
1.5k
views
Convert from plink or vcf to bgl format
vcf bgl plink
6.2 years ago by Mr Locuace ▴ 180
3
votes
1
reply
1.9k
views
Convert physical positions from Hg18 to Hg19
liftover
updated 6.3 years ago by 89k • written 6.3 years ago by ▴ 180
0
votes
0
replies
1.5k
views
Phasing genotype likelihood data and merging them with phased genotype calls data.
phasing genotype likelihood genotype calls
6.4 years ago by Mr Locuace ▴ 180
2
votes
1
reply
2.2k
views
Plink2. psam file missing in 1000G Phase3
plink2
updated 6.6 years ago by 11k • written 6.6 years ago by ▴ 180
0
votes
1
reply
65k
views
Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
6.6 years ago by Mr Locuace ▴ 180
8
votes
2
replies
2.8k
views
Get all SNPs that are in high linkage disequilibrium (based on D') for a set of SNPs
plink SNP LD
updated 6.7 years ago by 11k • written 6.7 years ago by ▴ 180
0
votes
0
replies
9.1k
views
Answer: A: How to calculate Hudson's Fst at Population and SNP level?
6.9 years ago by Mr Locuace ▴ 180
0
votes
0
replies
5.2k
views
Comment: A: Converting ms or msms output to PLINK or VCF files
6.9 years ago by Mr Locuace ▴ 180
0
votes
0
replies
1.5k
views
LD pruning before or after phasing for calculating site frequency spectrum?
SNP LD
7.0 years ago by Mr Locuace ▴ 180
0
votes
0
replies
7.7k
views
Comment: C: Merge two phased vcf files from 2 pops keeping same ref allele in merged file
7.0 years ago by Mr Locuace ▴ 180
6
votes
4
replies
6.7k
views
VCFtools. Get rid of DS:GP phased genotypes while keeping GT and remaining fields
VCFtools
7.1 years ago by Mr Locuace ▴ 180
0
votes
0
replies
1.3k
views
Run Husdon's ms with ABCtoolbox2.0
ABC ABCtoolbox Hudson ms
7.3 years ago by Mr Locuace ▴ 180
0
votes
0
replies
3.2k
views
Comment: C: Convert list of rs IDs from one format to another
7.4 years ago by Mr Locuace ▴ 180
3
votes
5
replies
3.2k
views
Convert list of rs IDs from one format to another
SNP identifiers eQTL GTEx
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 180
0
votes
0
replies
3.2k
views
Comment: C: Convert list of rs IDs from one format to another
7.4 years ago by Mr Locuace ▴ 180
0
votes
0
replies
3.4k
views
Comment: C: Get genomic coordinates for protein domain
7.4 years ago by Mr Locuace ▴ 180
0
votes
1
reply
3.4k
views
Comment: C: Get genomic coordinates for protein domain
7.4 years ago by Mr Locuace ▴ 180
3
votes
6
replies
3.4k
views
Get genomic coordinates for protein domain
protein domain coordinate
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 180
0
votes
0
replies
2.9k
views
Comment: C: Reference & alternative alleles extracted from 1000G, Phase 3
7.6 years ago by Mr Locuace ▴ 180
4
votes
5
replies
2.9k
views
Reference & alternative alleles extracted from 1000G, Phase 3
vcf 1000G ref allele
7.6 years ago by Mr Locuace ▴ 180
3
votes
0
replies
2.9k
views
Answer: A: Reference & alternative alleles extracted from 1000G, Phase 3
7.6 years ago by Mr Locuace ▴ 180
0
votes
0
replies
2.9k
views
Comment: C: Reference & alternative alleles extracted from 1000G, Phase 3
7.6 years ago by Mr Locuace ▴ 180
0
votes
0
replies
2.5k
views
Comment: C: Where to download official reference and alternative alleles from 1000 Genomes?
7.6 years ago by Mr Locuace ▴ 180
0
votes
1
reply
2.5k
views
Comment: C: Where to download official reference and alternative alleles from 1000 Genomes?
7.6 years ago by Mr Locuace ▴ 180
2
votes
6
replies
2.5k
views
Where to download official reference and alternative alleles from 1000 Genomes?
1000 Genomes reference allele Plink
updated 7.6 years ago by 11k • written 7.6 years ago by ▴ 180
0
votes
0
replies
1.5k
views
How to calculate the effective population size of part of a recently admixed genome?
effective population size SNP
7.7 years ago by Mr Locuace ▴ 180
0
votes
2
replies
9.7k
views
Comment: C: Convert vcf files with phased genotypes to standard haplotype format
7.7 years ago by Mr Locuace ▴ 180
13
votes
5
replies
9.7k
views
Convert vcf files with phased genotypes to standard haplotype format
haplotype vcf .hap
written 7.7 years ago by ▴ 180
0
votes
0
replies
2.9k
views
Comment: C: Plink. Convert ped files of artificially mixed population into vcf using recode
7.7 years ago by Mr Locuace ▴ 180
1
vote
2
replies
2.9k
views
Plink. Convert ped files of artificially mixed population into vcf using recode
Plink vcf phasing
updated 7.7 years ago by ▴ 240 • written 7.7 years ago by ▴ 180
3
votes
1
reply
2.6k
views
Plink. How to create small .ped file from big .ped file?
plink
updated 7.8 years ago by 11k • written 7.8 years ago by ▴ 180
1
vote
1
reply
5.3k
views
Comment: C: Why removing SNPs with MAF<5% for Fst calculation?
7.9 years ago by Mr Locuace ▴ 180
4
votes
7
replies
5.3k
views
Why removing SNPs with MAF<5% for Fst calculation?
snp maf Fst
updated 7.9 years ago by 89k • written 7.9 years ago by ▴ 180
1
vote
0
replies
7.9k
views
Comment: C: Using Plink, get allele frequencies for a subset of individuals
8.0 years ago by Mr Locuace ▴ 180
0
votes
1
reply
7.9k
views
Comment: C: Using Plink, get allele frequencies for a subset of individuals
8.0 years ago by Mr Locuace ▴ 180
67 results • Page 1 of 2
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