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1
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2
replies
2.6k
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bcftools merge is resulting in a lot of missing data, how do I fix this?
vcf bcf
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 740
7
votes
11
replies
12k
views
11 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink SNP
updated 10 months ago by • 0 • written 7.0 years ago by ▴ 740
0
votes
7
replies
1.5k
views
Cannot download BAMs from SRA AWS
bam
updated 2.0 years ago by 82k • written 2.0 years ago by ▴ 740
1
vote
5
replies
2.2k
views
How do I filter a multi-individual BCF file for genotype probabilities
vcf bcf
15 months ago by devenvyas ▴ 740
0
votes
0
replies
748
views
Getting frequencies for multiple SNPs from dbSNP at once?
dbSNP SNP
3.3 years ago by devenvyas ▴ 740
4
votes
2
replies
9.7k
views
VCFtools not filtering VCF file by positions
vcf vcftools SNP
updated 20 months ago by 43k • written 8.5 years ago by ▴ 740
0
votes
1
reply
758
views
Quick way of clearing out rs IDs from VCF?
VCF
3.5 years ago by devenvyas ▴ 740
1
vote
1
reply
2.0k
views
How do I plot RFMix results?
R
updated 3.6 years ago by ▴ 250 • written 4.2 years ago by ▴ 740
0
votes
1
reply
1.3k
views
Imputing missing genetic map distances from a bim file
plink SNP centimorgan
updated 3.6 years ago by • 0 • written 4.1 years ago by ▴ 740
0
votes
0
replies
971
views
How do I convert GPs to GLs?
imputation VCF
3.7 years ago by devenvyas ▴ 740
1
vote
3
replies
3.5k
views
Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)
SNP affymetrix human
updated 22 months ago by 43k • written 9.0 years ago by ▴ 740
1
vote
1
reply
1.3k
views
Getting centimorgan map units for 1000 Genomes data
plink
updated 4.1 years ago by 87k • written 4.1 years ago by ▴ 740
0
votes
0
replies
589
views
Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
IBD
4.3 years ago by devenvyas ▴ 740
0
votes
0
replies
573
views
Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?
ancientDNA BAM
4.5 years ago by devenvyas ▴ 740
0
votes
3
replies
1.8k
views
Clipping reads within BAM files?
bam
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by ▴ 740
0
votes
3
replies
2.0k
views
Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs. Ideas what is going on?
SNP
updated 18 months ago by 43k • written 8.8 years ago by ▴ 740
0
votes
1
reply
930
views
How do I get PyVCF to give me an error if the record it is fetching doesn't exist?
vcf
4.8 years ago by devenvyas ▴ 740
1
vote
0
replies
671
views
PCA on pairwise allele sharing counts
pca snp
4.9 years ago by devenvyas ▴ 740
0
votes
0
replies
792
views
Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
vcf snp
5.0 years ago by devenvyas ▴ 740
0
votes
1
reply
895
views
Constructing a Y chromosome phylogeny from VCF files
vcf phylogeny
updated 5.0 years ago by ▴ 60 • written 5.0 years ago by ▴ 740
3
votes
1
reply
4.6k
views
Two Plink map/ped files refuse to merge.
plink
updated 16 months ago by 43k • written 8.9 years ago by ▴ 740
5
votes
6
replies
3.6k
views
Scatter plot when there is a standard error for both axes
R
updated 21 months ago by 43k • written 8.3 years ago by ▴ 740
16
votes
5
replies
12k
views
What is a bad GATK Genotype Quality?
quality SNP
updated 16 months ago by 43k • written 8.9 years ago by ▴ 740
2
votes
7
replies
15k
views
Generating an ADMIXTURE plot that stacks the different values of K using R
R ADMIXTURE
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 740
2
votes
5
replies
8.6k
views
Converting list of Affy SNP ids to dbSNP rs ids
rs SNP affymetrix
updated 22 months ago by 43k • written 9.0 years ago by ▴ 740
4
votes
2
replies
4.2k
views
Help getting Plink files into Treemix
plink SNP
updated 6.0 years ago by 20 • written 8.0 years ago by ▴ 740
2
votes
2
replies
3.0k
views
Should replicate analyses of ADMIXTURE all have the same cross-validation values
admixture
updated 21 months ago by 43k • written 8.3 years ago by ▴ 740
1
vote
1
reply
1.3k
views
When did SNP genotyping arrays first come into use in research?
SNP
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 740
3
votes
9
replies
2.5k
views
ANNOVAR is losing 886 SNPs, and I can't figure out why
SNP
7.0 years ago by devenvyas ▴ 740
0
votes
3
replies
1.7k
views
Need help plotting D statistics
R
7.1 years ago by devenvyas ▴ 740
0
votes
2
replies
2.6k
views
Using Sequin, cannot put in protein translation exception.
sequin genbank mitochondrial genome
updated 7.2 years ago by • 0 • written 9.6 years ago by ▴ 740
4
votes
7
replies
6.0k
views
Help making ADMIXTURE output digestible
admixture
updated 11 months ago by ▴ 20 • written 8.8 years ago by ▴ 740
2
votes
11
replies
2.9k
views
Where can I upload SNP array data for public accessibility?
SNP
updated 7.5 years ago by ★ 4.9k • written 7.5 years ago by ▴ 740
0
votes
0
replies
1.4k
views
Figuring out if populations from two regions share the same Neanderthal haplotypes...
snp
updated 7.6 years ago by 20 • written 7.8 years ago by ▴ 740
0
votes
7
replies
3.3k
views
Getting p-values for whether the allele frequencies from two or more populations for 1800 SNPs are different
snp
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 740
0
votes
3
replies
1.3k
views
Figuring out which genes a set of SNPs overlap with
gene SNP
updated 7.7 years ago by 47k • written 7.7 years ago by ▴ 740
3
votes
3
replies
6.3k
views
Good way to graph allele frequency of different SNPs along chromosomes
SNP allele
7.7 years ago by devenvyas ▴ 740
1
vote
1
reply
3.3k
views
Convert Plink files to UCSC BED files
snp UCSC
updated 7.7 years ago by 4.2k • written 7.7 years ago by ▴ 740
0
votes
0
replies
1.9k
views
Calculating allele frequency differences between two populations at sites across the genome
snp genome Plink
7.7 years ago by devenvyas ▴ 740
1
vote
3
replies
5.0k
views
How does Plink choose which SNP is Allele1 and Allele2?
plink R
updated 7.7 years ago by 10k • written 7.7 years ago by ▴ 740
2
votes
4
replies
2.4k
views
Where do you cite R packages such as ggmap in a manuscript?
R
7.7 years ago by devenvyas ▴ 740
3
votes
5
replies
2.3k
views
Good repository for uploading SNP data (from genotyping array) alongside manuscript?
SNP
7.8 years ago by devenvyas ▴ 740
1
vote
4
replies
1.7k
views
Good text or video explaining what sequence alignment is to an undergrad
alignment
7.8 years ago by devenvyas ▴ 740
1
vote
1
reply
1.8k
views
How to compare Neanderthal ancestry blocks between two sets of populations using SNP data
Neanderthal SNP ancestry
updated 7.8 years ago by ★ 4.0k • written 8.0 years ago by ▴ 740
0
votes
0
replies
2.3k
views
Creating a tree from pairwise FST values for ADMIXTURE components
FST
7.8 years ago by devenvyas ▴ 740
0
votes
0
replies
1.7k
views
Filter VCF data to merge with SNP array data - good filter settings?
snp genome vcf plink
updated 7.9 years ago by 20 • written 8.0 years ago by ▴ 740
0
votes
0
replies
2.4k
views
Setting two outgroups in Treemix
treemix
8.0 years ago by devenvyas ▴ 740
2
votes
1
reply
2.0k
views
Does Treemix support multithreaded analyses?
treemix SNP
8.0 years ago by devenvyas ▴ 740
0
votes
0
replies
1.6k
views
Is there a way to filter Plink files based off a cluster file
SNP Plink
8.0 years ago by devenvyas ▴ 740
0
votes
0
replies
1.3k
views
Filtering Plink files by coordinate as opposed to SNP id?
plink SNP
8.0 years ago by devenvyas ▴ 740
95 results • Page 1 of 2
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