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1
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2
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2.5k
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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 9 months ago by • 0 • written 6.9 years ago by ▴ 740
0
votes
0
replies
2.1k
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Comment: Comment: How do I filter a multi-individual BCF file for genotype probabilities
15 months ago by devenvyas ▴ 740
0
votes
0
replies
2.1k
views
Comment: Comment: How do I filter a multi-individual BCF file for genotype probabilities
15 months ago by devenvyas ▴ 740
0
votes
1
reply
1.5k
views
Comment: Comment: Cannot download BAMs from SRA AWS
2.0 years ago by devenvyas ▴ 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
0
votes
0
replies
1.5k
views
Comment: Comment: Cannot download BAMs from SRA AWS
2.0 years ago by devenvyas ▴ 740
1
vote
5
replies
2.1k
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
741
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
755
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 3.5 years ago by ▴ 250 • written 4.1 years ago by ▴ 740
0
votes
1
reply
1.2k
views
Imputing missing genetic map distances from a bim file
plink SNP centimorgan
updated 3.6 years ago by • 0 • written 4.0 years ago by ▴ 740
0
votes
0
replies
965
views
How do I convert GPs to GLs?
imputation VCF
3.7 years ago by devenvyas ▴ 740
1
vote
3
replies
3.4k
views
Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)
SNP affymetrix human
updated 21 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 4.0 years ago by 87k • written 4.0 years ago by ▴ 740
0
votes
0
replies
3.3k
views
Comment: C: Plot local ancestry on chromosome
4.1 years ago by devenvyas ▴ 740
0
votes
0
replies
587
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
4.1k
views
Comment: C: Help needed parsing VCF files
updated 4.3 years ago by 43k • written 9.9 years ago by ▴ 740
0
votes
1
reply
3.5k
views
Comment: C: Scatter plot when there is a standard error for both axes
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 740
0
votes
0
replies
2.5k
views
Comment: C: Extracting SNP data for specific rs#s from published genome sequences
updated 4.3 years ago by 43k • written 10.0 years ago by ▴ 740
0
votes
1
reply
1.9k
views
Comment: C: Good way of plotting a statistic with error bars
updated 4.3 years ago by 43k • written 8.3 years ago by ▴ 740
0
votes
0
replies
5.8k
views
Comment: C: Updating dbSNP rs ids from old SNP data
updated 4.4 years ago by 43k • written 8.7 years ago by ▴ 740
0
votes
1
reply
4.3k
views
Comment: A: How to obtain ancestral alleles based on Hg19 genome coordinates?
updated 4.4 years ago by 43k • written 8.5 years ago by ▴ 740
4
votes
0
replies
9.7k
views
Answer: A: VCFtools not filtering VCF file by positions
updated 4.4 years ago by 43k • written 8.5 years ago by ▴ 740
1
vote
1
reply
4.5k
views
Comment: C: New to SNP data: I need help getting Affy Axiom data out of genotyping console i
updated 4.4 years ago by 43k • written 8.5 years ago by ▴ 740
0
votes
1
reply
1.7k
views
Comment: C: Clipping reads within BAM files?
4.5 years ago by devenvyas ▴ 740
0
votes
0
replies
571
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
1.7k
views
Clipping reads within BAM files?
bam
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by ▴ 740
0
votes
0
replies
2.0k
views
Comment: C: Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs
updated 4.5 years ago by 43k • written 8.7 years ago by ▴ 740
0
votes
0
replies
2.0k
views
Comment: C: Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs
updated 4.5 years ago by 43k • written 8.7 years ago by ▴ 740
0
votes
0
replies
4.0k
views
Comment: C: Large tab-delimited table of SNP data, how to filter out some rows based on rsID
updated 4.5 years ago by 43k • written 8.8 years ago by ▴ 740
0
votes
0
replies
3.9k
views
Comment: C: Need good way to run a Principle Component Analysis on SNP data
updated 4.5 years ago by 43k • written 8.8 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 8.7 years ago by ▴ 740
0
votes
1
reply
921
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
669
views
PCA on pairwise allele sharing counts
pca snp
4.9 years ago by devenvyas ▴ 740
0
votes
0
replies
4.0k
views
Comment: C: Problems with vcf-merge
updated 4.9 years ago by 43k • written 9.9 years ago by ▴ 740
0
votes
0
replies
789
views
Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
vcf snp
4.9 years ago by devenvyas ▴ 740
0
votes
1
reply
889
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 8.8 years ago by ▴ 740
5
votes
6
replies
3.5k
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 8.8 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
0
votes
1
reply
15k
views
Comment: C: Generating an ADMIXTURE plot that stacks the different values of K using R
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 740
0
votes
0
replies
15k
views
Comment: C: Generating an ADMIXTURE plot that stacks the different values of K using R
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 21 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
2.9k
views
Should replicate analyses of ADMIXTURE all have the same cross-validation values
admixture
updated 21 months ago by 43k • written 8.2 years ago by ▴ 740
1
vote
1
reply
1.3k
views
When did SNP genotyping arrays first come into use in research?
SNP
updated 6.9 years ago by ★ 2.8k • written 6.9 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
213 results • Page 1 of 5
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