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1
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2
replies
2.1k
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What are good settings to filter VCF files to merge SNP data with SNP array data
vcf SNP
updated 8.1 years ago by ★ 3.8k • written 8.1 years ago by ▴ 740
3
votes
2
replies
3.7k
views
Why is my ADMIXTURE random seed always 43
ADMIXTURE
updated 8.3 years ago by 22k • written 8.3 years ago by ▴ 740
1
vote
5
replies
1.9k
views
Good way of plotting a statistic with error bars
plot
updated 21 months ago by 43k • written 8.4 years ago by ▴ 740
0
votes
2
replies
2.3k
views
Perplexing ADMIXTURE results - one component present at K =10 disappears at 11, reappears at 12
SNP ADMIXTURE
updated 21 months ago by 43k • written 8.4 years ago by ▴ 740
2
votes
5
replies
5.2k
views
Downloading synonyms for dbSNP rsids
dbSNP SNP
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 740
0
votes
0
replies
1.6k
views
Seeking different methods of estimating Neanderthal ancestry in modern human SNP data
SNP Neanderthal admixtools
updated 21 months ago by 43k • written 8.5 years ago by ▴ 740
8
votes
13
replies
5.9k
views
6 follow
Updating dbSNP rs ids from old SNP data
snp dbSNP
updated 19 months ago by 43k • written 8.8 years ago by ▴ 740
1
vote
1
reply
4.2k
views
Filtering a VCF based on Map Quality
vcf SNP
updated 21 months ago by 43k • written 8.6 years ago by ▴ 740
2
votes
2
replies
2.2k
views
Filtering down 1000 Genomes data just for a set of SNPs
vcf SNP
updated 21 months ago by 43k • written 8.6 years ago by ▴ 740
2
votes
4
replies
4.3k
views
How to obtain ancestral alleles based on Hg19 genome coordinates?
SNP
updated 21 months ago by 43k • written 8.6 years ago by ▴ 740
1
vote
8
replies
3.3k
views
Efficient means of mass converting Affy SNP IDs to dbSNP rs ids
affy dbSNP Perl Bash Python
updated 16 months ago by 43k • written 9.0 years ago by ▴ 740
0
votes
1
reply
2.1k
views
Good way of obtaining Human-Chimp ancestral genotypes?
SNP
updated 20 months ago by 43k • written 8.6 years ago by ▴ 740
1
vote
5
replies
4.5k
views
New to SNP data: I need help getting Affy Axiom data out of genotyping console into a Principle Component Analysis
Affymetrix SNP
updated 14 months ago by 43k • written 9.1 years ago by ▴ 740
0
votes
0
replies
1.8k
views
Looking for a quick way of consistently order components between different ADMIXTURE analyses
admixture
updated 20 months ago by 43k • written 8.7 years ago by ▴ 740
4
votes
2
replies
2.8k
views
Change output name for ADMIXTURE analysis
admixture
updated 20 months ago by 43k • written 8.7 years ago by ▴ 740
0
votes
1
reply
4.2k
views
What is a bad lowest-CV value for Admixture?
admixture SNP CV
updated 19 months ago by 43k • written 8.8 years ago by ▴ 740
0
votes
0
replies
3.1k
views
Set uniform bar widths for ADMIXTURE barplots in R
admixture R
updated 19 months ago by 43k • written 8.8 years ago by ▴ 740
0
votes
3
replies
4.6k
views
Plink file coded in 1/2/3/4 - how do I convert to ACGT
plink SNP
updated 18 months ago by 43k • written 8.9 years ago by ▴ 740
4
votes
6
replies
4.3k
views
ADMIXTURE results - how can I determine what SNPs are associated with different inferred ancestry components?
SNP ADMIXTURE
updated 19 months ago by 43k • written 8.8 years ago by ▴ 740
0
votes
3
replies
5.9k
views
Setting dimensions of barplot area in R (for STRUCTURE-like plot)
R
updated 19 months ago by 43k • written 8.8 years ago by ▴ 740
3
votes
4
replies
4.5k
views
How to tell Plink to merge based on Hg19 coordinates, not based on SNP ID
plink SNP
updated 8.8 years ago by ★ 2.3k • written 8.8 years ago by ▴ 740
0
votes
0
replies
1.9k
views
Changing sample phenotypes in Plink
plink SNP
8.8 years ago by devenvyas ▴ 740
5
votes
4
replies
2.5k
views
Help merging VCF files divided by chromosome
vcf python
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
5
votes
1
reply
2.2k
views
Merging datasets from different arrays - need quick way to generate the intersection of intersections
shell python SNP R
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
0
votes
2
replies
3.1k
views
Are Plink MDS plots supposed to complete so quickly?
plink SNP mds
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
3
votes
3
replies
4.6k
views
Merging two Plink datasets, but some sites have reversed genotypes
plink SNP
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
1
vote
11
replies
3.9k
views
Need good way to run a Principle Component Analysis on SNP data
pca SNP
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
0
votes
0
replies
1.9k
views
Axiom sample call-rate cut-off strictly 97%?
SNP affymetrix
updated 17 months ago by 43k • written 8.9 years ago by ▴ 740
6
votes
12
replies
9.2k
views
Coding genotypes from nucleotides to 0/1/2 in R.
SNP R
updated 16 months ago by 43k • written 8.9 years ago by ▴ 740
4
votes
17
replies
6.0k
views
Need help transposing MAP file and PED file into one large table
SNP Python Bash
updated 16 months ago by 43k • written 8.9 years ago by ▴ 740
5
votes
14
replies
4.0k
views
Large tab-delimited table of SNP data, how to filter out some rows based on rsIDs?
rsid python SNP
updated 16 months ago by 43k • written 9.0 years ago by ▴ 740
0
votes
2
replies
3.8k
views
Affy Axiom array - many cases of two probe set IDs sharing the same Affy SNP ID and dbSNP RS ID values. What's going on?
SNP Affymetrix
updated 22 months ago by 43k • written 9.1 years ago by ▴ 740
0
votes
0
replies
1.8k
views
Regarding Affymetrix Axiom DNA 260/280 and 260/230 value requirements
nanodrop
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 740
3
votes
5
replies
2.1k
views
Getting the intersection of two dbSNP lists
snp
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 740
0
votes
8
replies
4.3k
views
Need code to filter VCF files based on rsid using Pysam
vcf python dbSNP
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 740
0
votes
0
replies
1.8k
views
Annotating human mitogenomes for submission to GenBank; do I need to annotate everything?
sequin genbank annotate
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 740
0
votes
0
replies
2.0k
views
Using Sequin, how to delete column in alignment
sequin genbank
updated 3.2 years ago by 43k • written 9.6 years ago by ▴ 740
37
votes
6
replies
19k
views
What are good settings for filtering VCF files?
samtools vcftools SNP bcftools
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 740
5
votes
2
replies
3.2k
views
Question about dbSNP rs #s
rs genome dbSNP SNP coordinates
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 740
3
votes
4
replies
2.9k
views
Protocol for calling SNPs from a large number of BAM files
BAM VCF SNP
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 740
1
vote
5
replies
4.0k
views
Problems with vcf-merge
vcftools vcf SNP
updated 2.6 years ago by 43k • written 10.0 years ago by ▴ 740
1
vote
11
replies
4.1k
views
Help needed parsing VCF files
SNP tabix VCF rs
updated 2.6 years ago by 43k • written 9.9 years ago by ▴ 740
1
vote
1
reply
3.0k
views
VCF file lacks alternative allele listing for most rs ids
vcftools VCF dbSNP SNP
updated 2.7 years ago by 43k • written 10.0 years ago by ▴ 740
28
votes
3
replies
21k
views
Filtering a vcf file with vcftools, where is my output?
vcftools vcf SNP
updated 2.7 years ago by 43k • written 10.0 years ago by ▴ 740
1
vote
2
replies
2.5k
views
Extracting SNP data for specific rs#s from published genome sequences
snp genome
updated 2.3 years ago by 43k • written 10.0 years ago by ▴ 740
95 results • Page 2 of 2
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