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0
votes
2
replies
783
views
Converting GRCh38 30× 1000G data to GRCh37
bam 1000Genomes alignment
updated 16 months ago by 45k • written 16 months ago by ▴ 770
1
vote
0
replies
342
views
Calculating F_IS, F_IT on ancient DNA
adna
17 months ago by devenvyas ▴ 770
1
vote
2
replies
4.7k
views
bcftools merge is resulting in a lot of missing data, how do I fix this?
vcf bcf
updated 2.2 years ago by • 0 • written 4.6 years ago by ▴ 770
9
votes
11
replies
16k
views
11 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink SNP
updated 2.4 years ago by ▴ 10 • written 8.5 years ago by ▴ 770
0
votes
8
replies
2.9k
views
6 follow
Cannot download BAMs from SRA AWS
bam
updated 16 months ago by ▴ 20 • written 3.6 years ago by ▴ 770
1
vote
5
replies
3.4k
views
How do I filter a multi-individual BCF file for genotype probabilities
vcf bcf
2.8 years ago by devenvyas ▴ 770
0
votes
0
replies
956
views
Getting frequencies for multiple SNPs from dbSNP at once?
dbSNP SNP
4.8 years ago by devenvyas ▴ 770
4
votes
2
replies
11k
views
VCFtools not filtering VCF file by positions
vcf vcftools SNP
updated 3.2 years ago by 45k • written 10.1 years ago by ▴ 770
0
votes
1
reply
1.0k
views
Quick way of clearing out rs IDs from VCF?
VCF
5.1 years ago by devenvyas ▴ 770
1
vote
1
reply
2.7k
views
How do I plot RFMix results?
R
updated 5.1 years ago by ▴ 270 • written 5.7 years ago by ▴ 770
0
votes
1
reply
1.7k
views
Imputing missing genetic map distances from a bim file
plink SNP centimorgan
updated 5.2 years ago by • 0 • written 5.6 years ago by ▴ 770
0
votes
0
replies
1.3k
views
How do I convert GPs to GLs?
imputation VCF
5.2 years ago by devenvyas ▴ 770
1
vote
3
replies
4.4k
views
Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)
SNP affymetrix human
updated 3.4 years ago by 45k • written 10.6 years ago by ▴ 770
1
vote
1
reply
1.7k
views
Getting centimorgan map units for 1000 Genomes data
plink
updated 5.6 years ago by 90k • written 5.6 years ago by ▴ 770
0
votes
0
replies
806
views
Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
IBD
5.8 years ago by devenvyas ▴ 770
0
votes
0
replies
790
views
Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?
ancientDNA BAM
6.0 years ago by devenvyas ▴ 770
0
votes
3
replies
2.5k
views
Clipping reads within BAM files?
bam
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by ▴ 770
0
votes
3
replies
2.5k
views
Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs. Ideas what is going on?
SNP
updated 3.1 years ago by 45k • written 10.3 years ago by ▴ 770
0
votes
1
reply
1.2k
views
How do I get PyVCF to give me an error if the record it is fetching doesn't exist?
vcf
6.4 years ago by devenvyas ▴ 770
1
vote
0
replies
860
views
PCA on pairwise allele sharing counts
pca snp
6.4 years ago by devenvyas ▴ 770
0
votes
0
replies
1.0k
views
Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
vcf snp
6.5 years ago by devenvyas ▴ 770
0
votes
1
reply
1.3k
views
Constructing a Y chromosome phylogeny from VCF files
vcf phylogeny
updated 6.5 years ago by ▴ 60 • written 6.6 years ago by ▴ 770
3
votes
1
reply
5.0k
views
Two Plink map/ped files refuse to merge.
plink
updated 2.9 years ago by 45k • written 10.4 years ago by ▴ 770
5
votes
6
replies
4.2k
views
Scatter plot when there is a standard error for both axes
R
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 770
16
votes
5
replies
14k
views
What is a bad GATK Genotype Quality?
quality SNP
updated 2.9 years ago by 45k • written 10.4 years ago by ▴ 770
3
votes
7
replies
16k
views
Generating an ADMIXTURE plot that stacks the different values of K using R
R ADMIXTURE
updated 7.2 years ago by 45k • written 9.7 years ago by ▴ 770
2
votes
5
replies
10.0k
views
Converting list of Affy SNP ids to dbSNP rs ids
rs SNP affymetrix
updated 3.4 years ago by 45k • written 10.5 years ago by ▴ 770
4
votes
2
replies
4.8k
views
Help getting Plink files into Treemix
plink SNP
updated 7.5 years ago by 20 • written 9.6 years ago by ▴ 770
2
votes
2
replies
3.6k
views
Should replicate analyses of ADMIXTURE all have the same cross-validation values
admixture
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 770
1
vote
1
reply
1.8k
views
When did SNP genotyping arrays first come into use in research?
SNP
updated 8.5 years ago by ★ 2.8k • written 8.5 years ago by ▴ 770
3
votes
9
replies
3.5k
views
ANNOVAR is losing 886 SNPs, and I can't figure out why
SNP
8.6 years ago by devenvyas ▴ 770
0
votes
3
replies
2.3k
views
Need help plotting D statistics
R
8.6 years ago by devenvyas ▴ 770
0
votes
2
replies
3.2k
views
Using Sequin, cannot put in protein translation exception.
sequin genbank mitochondrial genome
updated 8.7 years ago by • 0 • written 11.1 years ago by ▴ 770
4
votes
7
replies
8.0k
views
Help making ADMIXTURE output digestible
admixture
updated 2.5 years ago by ▴ 20 • written 10.3 years ago by ▴ 770
2
votes
11
replies
3.9k
views
Where can I upload SNP array data for public accessibility?
SNP
updated 9.0 years ago by ★ 5.0k • written 9.0 years ago by ▴ 770
0
votes
0
replies
1.6k
views
Figuring out if populations from two regions share the same Neanderthal haplotypes...
snp
updated 9.1 years ago by 20 • written 9.3 years ago by ▴ 770
0
votes
7
replies
4.0k
views
Getting p-values for whether the allele frequencies from two or more populations for 1800 SNPs are different
snp
updated 9.2 years ago by ★ 1.2k • written 9.2 years ago by ▴ 770
0
votes
3
replies
1.6k
views
Figuring out which genes a set of SNPs overlap with
gene SNP
updated 9.2 years ago by 48k • written 9.2 years ago by ▴ 770
3
votes
3
replies
7.3k
views
Good way to graph allele frequency of different SNPs along chromosomes
SNP allele
9.2 years ago by devenvyas ▴ 770
1
vote
1
reply
3.8k
views
Convert Plink files to UCSC BED files
snp UCSC
updated 9.3 years ago by 4.8k • written 9.3 years ago by ▴ 770
0
votes
0
replies
2.1k
views
Calculating allele frequency differences between two populations at sites across the genome
snp genome Plink
9.3 years ago by devenvyas ▴ 770
1
vote
3
replies
6.3k
views
How does Plink choose which SNP is Allele1 and Allele2?
plink R
updated 9.3 years ago by 11k • written 9.3 years ago by ▴ 770
2
votes
4
replies
2.9k
views
Where do you cite R packages such as ggmap in a manuscript?
R
9.3 years ago by devenvyas ▴ 770
3
votes
5
replies
3.1k
views
Good repository for uploading SNP data (from genotyping array) alongside manuscript?
SNP
9.3 years ago by devenvyas ▴ 770
1
vote
4
replies
2.2k
views
Good text or video explaining what sequence alignment is to an undergrad
alignment
9.3 years ago by devenvyas ▴ 770
1
vote
1
reply
2.1k
views
How to compare Neanderthal ancestry blocks between two sets of populations using SNP data
Neanderthal SNP ancestry
updated 9.4 years ago by ★ 4.0k • written 9.6 years ago by ▴ 770
0
votes
0
replies
2.6k
views
Creating a tree from pairwise FST values for ADMIXTURE components
FST
9.4 years ago by devenvyas ▴ 770
0
votes
0
replies
1.9k
views
Filter VCF data to merge with SNP array data - good filter settings?
snp genome vcf plink
updated 9.4 years ago by 20 • written 9.6 years ago by ▴ 770
0
votes
0
replies
2.7k
views
Setting two outgroups in Treemix
treemix
9.5 years ago by devenvyas ▴ 770
2
votes
1
reply
2.3k
views
Does Treemix support multithreaded analyses?
treemix SNP
9.5 years ago by devenvyas ▴ 770
97 results • Page 1 of 2
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