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1
reply
3.0k
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Comment: Comment: Realigning BAM files to new reference
10 months ago by devenvyas ▴ 770
0
votes
2
replies
527
views
Converting GRCh38 30× 1000G data to GRCh37
bam 1000Genomes alignment
updated 10 months ago by 45k • written 10 months ago by ▴ 770
1
vote
0
replies
250
views
Calculating F_IS, F_IT on ancient DNA
adna
11 months ago by devenvyas ▴ 770
1
vote
2
replies
3.7k
views
bcftools merge is resulting in a lot of missing data, how do I fix this?
vcf bcf
updated 19 months ago by • 0 • written 4.0 years ago by ▴ 770
9
votes
11
replies
14k
views
11 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink SNP
updated 22 months ago by ▴ 10 • written 8.0 years ago by ▴ 770
0
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0
replies
2.9k
views
Comment: Comment: How do I filter a multi-individual BCF file for genotype probabilities
2.3 years ago by devenvyas ▴ 770
0
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0
replies
2.9k
views
Comment: Comment: How do I filter a multi-individual BCF file for genotype probabilities
2.3 years ago by devenvyas ▴ 770
0
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1
reply
2.2k
views
Comment: Comment: Cannot download BAMs from SRA AWS
3.0 years ago by devenvyas ▴ 770
0
votes
8
replies
2.2k
views
6 follow
Cannot download BAMs from SRA AWS
bam
updated 9 months ago by ▴ 20 • written 3.0 years ago by ▴ 770
0
votes
0
replies
2.2k
views
Comment: Comment: Cannot download BAMs from SRA AWS
3.0 years ago by devenvyas ▴ 770
1
vote
5
replies
2.9k
views
How do I filter a multi-individual BCF file for genotype probabilities
vcf bcf
2.3 years ago by devenvyas ▴ 770
0
votes
0
replies
871
views
Getting frequencies for multiple SNPs from dbSNP at once?
dbSNP SNP
4.3 years ago by devenvyas ▴ 770
4
votes
2
replies
11k
views
VCFtools not filtering VCF file by positions
vcf vcftools SNP
updated 2.7 years ago by 45k • written 9.5 years ago by ▴ 770
0
votes
1
reply
914
views
Quick way of clearing out rs IDs from VCF?
VCF
4.5 years ago by devenvyas ▴ 770
1
vote
1
reply
2.5k
views
How do I plot RFMix results?
R
updated 4.6 years ago by ▴ 270 • written 5.1 years ago by ▴ 770
0
votes
1
reply
1.5k
views
Imputing missing genetic map distances from a bim file
plink SNP centimorgan
updated 4.6 years ago by • 0 • written 5.0 years ago by ▴ 770
0
votes
0
replies
1.1k
views
How do I convert GPs to GLs?
imputation VCF
4.7 years ago by devenvyas ▴ 770
1
vote
3
replies
4.0k
views
Just got back raw Affy Axiom SNP data from core lab, where do I start? (new learner)
SNP affymetrix human
updated 2.8 years ago by 45k • written 10.0 years ago by ▴ 770
1
vote
1
reply
1.5k
views
Getting centimorgan map units for 1000 Genomes data
plink
updated 5.0 years ago by 89k • written 5.0 years ago by ▴ 770
0
votes
0
replies
3.8k
views
Comment: C: Plot local ancestry on chromosome
5.1 years ago by devenvyas ▴ 770
0
votes
0
replies
708
views
Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
IBD
5.3 years ago by devenvyas ▴ 770
0
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0
replies
4.8k
views
Comment: C: Help needed parsing VCF files
updated 5.3 years ago by 45k • written 10.9 years ago by ▴ 770
0
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1
reply
3.9k
views
Comment: C: Scatter plot when there is a standard error for both axes
updated 5.3 years ago by 45k • written 9.3 years ago by ▴ 770
0
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0
replies
2.7k
views
Comment: C: Extracting SNP data for specific rs#s from published genome sequences
updated 5.3 years ago by 45k • written 11.0 years ago by ▴ 770
0
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1
reply
2.3k
views
Comment: C: Good way of plotting a statistic with error bars
updated 5.4 years ago by 45k • written 9.3 years ago by ▴ 770
0
votes
0
replies
6.8k
views
Comment: C: Updating dbSNP rs ids from old SNP data
updated 5.4 years ago by 45k • written 9.7 years ago by ▴ 770
0
votes
1
reply
4.7k
views
Comment: A: How to obtain ancestral alleles based on Hg19 genome coordinates?
updated 5.4 years ago by 45k • written 9.5 years ago by ▴ 770
4
votes
0
replies
11k
views
Answer: A: VCFtools not filtering VCF file by positions
updated 5.4 years ago by 45k • written 9.5 years ago by ▴ 770
1
vote
1
reply
5.2k
views
Comment: C: New to SNP data: I need help getting Affy Axiom data out of genotyping console i
updated 5.4 years ago by 45k • written 9.5 years ago by ▴ 770
0
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1
reply
2.2k
views
Comment: C: Clipping reads within BAM files?
5.5 years ago by devenvyas ▴ 770
0
votes
0
replies
672
views
Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?
ancientDNA BAM
5.5 years ago by devenvyas ▴ 770
0
votes
3
replies
2.2k
views
Clipping reads within BAM files?
bam
updated 5.5 years ago by ★ 1.4k • written 5.5 years ago by ▴ 770
0
votes
0
replies
2.3k
views
Comment: C: Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs
updated 5.5 years ago by 45k • written 9.8 years ago by ▴ 770
0
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0
replies
2.3k
views
Comment: C: Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs
updated 5.5 years ago by 45k • written 9.8 years ago by ▴ 770
0
votes
0
replies
4.7k
views
Comment: C: Large tab-delimited table of SNP data, how to filter out some rows based on rsID
updated 5.5 years ago by 45k • written 9.9 years ago by ▴ 770
0
votes
0
replies
4.6k
views
Comment: C: Need good way to run a Principle Component Analysis on SNP data
updated 5.5 years ago by 45k • written 9.9 years ago by ▴ 770
0
votes
3
replies
2.3k
views
Merging sets of autosomal SNPs from the same array, but I am losing ~50,000 SNPs. Ideas what is going on?
SNP
updated 2.5 years ago by 45k • written 9.8 years ago by ▴ 770
0
votes
1
reply
1.1k
views
How do I get PyVCF to give me an error if the record it is fetching doesn't exist?
vcf
5.8 years ago by devenvyas ▴ 770
1
vote
0
replies
765
views
PCA on pairwise allele sharing counts
pca snp
5.9 years ago by devenvyas ▴ 770
0
votes
0
replies
4.3k
views
Comment: C: Problems with vcf-merge
updated 5.9 years ago by 45k • written 11.0 years ago by ▴ 770
0
votes
0
replies
890
views
Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
vcf snp
6.0 years ago by devenvyas ▴ 770
0
votes
1
reply
1.1k
views
Constructing a Y chromosome phylogeny from VCF files
vcf phylogeny
updated 6.0 years ago by ▴ 60 • written 6.0 years ago by ▴ 770
3
votes
1
reply
4.9k
views
Two Plink map/ped files refuse to merge.
plink
updated 2.4 years ago by 45k • written 9.9 years ago by ▴ 770
5
votes
6
replies
3.9k
views
Scatter plot when there is a standard error for both axes
R
updated 2.8 years ago by 45k • written 9.3 years ago by ▴ 770
16
votes
5
replies
13k
views
What is a bad GATK Genotype Quality?
quality SNP
updated 2.4 years ago by 45k • written 9.8 years ago by ▴ 770
3
votes
7
replies
15k
views
Generating an ADMIXTURE plot that stacks the different values of K using R
R ADMIXTURE
updated 6.6 years ago by 45k • written 9.2 years ago by ▴ 770
0
votes
1
reply
15k
views
Comment: C: Generating an ADMIXTURE plot that stacks the different values of K using R
updated 6.6 years ago by 45k • written 9.2 years ago by ▴ 770
0
votes
0
replies
15k
views
Comment: C: Generating an ADMIXTURE plot that stacks the different values of K using R
updated 6.6 years ago by 45k • written 9.2 years ago by ▴ 770
2
votes
5
replies
9.4k
views
Converting list of Affy SNP ids to dbSNP rs ids
rs SNP affymetrix
updated 2.8 years ago by 45k • written 10.0 years ago by ▴ 770
4
votes
2
replies
4.6k
views
Help getting Plink files into Treemix
plink SNP
updated 7.0 years ago by 20 • written 9.0 years ago by ▴ 770
216 results • Page 1 of 5
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