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1
vote
0
replies
201
views
Forum:
Penetrance versus heritability
penetrance
heritability
3 months ago by
tacrolimus
▴ 110
1
vote
0
replies
184
views
Meta-analysis of rare variant SAIGE-GENE output for WGS data
meta-analysis
rare
SAIGE
variant
4 months ago by
tacrolimus
▴ 110
0
votes
1
reply
478
views
Comment:
Comment: Counting the specific number of a type of variant per sample in a multi-sample
4 months ago by
tacrolimus
▴ 110
5
votes
3
replies
478
views
Counting the specific number of a type of variant per sample in a multi-sample VCF
bcftools
VCF
updated 4 months ago by
Pierre Lindenbaum
155k • written 4 months ago by
tacrolimus
▴ 110
0
votes
0
replies
343
views
Comment:
Comment: Ascertaining whether polygenic risk score is statistically independent to a mono
7 months ago by
tacrolimus
▴ 110
4
votes
2
replies
343
views
Ascertaining whether polygenic risk score is statistically independent to a monogenic risk
polygenic
score
PRS
risk
SAIGE
7 months ago by
tacrolimus
▴ 110
3
votes
1
reply
339
views
Pathway analysis using rare-variant SKAT-O summary statistics
variant
rare
pathway
analysis
R
updated 7 months ago by
LChart
2.7k • written 7 months ago by
tacrolimus
▴ 110
0
votes
0
replies
419
views
Comment:
Comment: Basic PRS question
8 months ago by
tacrolimus
▴ 110
0
votes
1
reply
419
views
Comment:
Comment: Basic PRS question
8 months ago by
tacrolimus
▴ 110
0
votes
4
replies
419
views
Basic PRS question
PRS
8 months ago by
tacrolimus
▴ 110
0
votes
0
replies
457
views
Running a validated polygenic risk score (PRS) on a new dataset using VCF/PGEN files (in the 100K genomes project)
PRS
polygenic
risk
score
8 months ago by
tacrolimus
▴ 110
0
votes
2
replies
1.3k
views
Counting allele counts/frequencies from a vcf file with both cases and controls
bcftools
allele count
vep
updated 16 months ago by
Paolo
• 0 • written 2.8 years ago by
tacrolimus
▴ 110
0
votes
0
replies
350
views
Answer:
Answer: Ancient DNA Analysis Fastq to vcf
16 months ago by
tacrolimus
▴ 110
0
votes
0
replies
319
views
Power calculation for a collapsing rare variant analysis
calculation
SAIGE
power
rare
variant
collapsing
test
16 months ago by
tacrolimus
▴ 110
0
votes
0
replies
789
views
Comment:
Comment: Creating a per sample file from multi-sample vcf
18 months ago by
tacrolimus
▴ 110
0
votes
1
reply
789
views
Comment:
Comment: Creating a per sample file from multi-sample vcf
18 months ago by
tacrolimus
▴ 110
0
votes
1
reply
789
views
Comment:
Comment: Creating a per sample file from multi-sample vcf
18 months ago by
tacrolimus
▴ 110
4
votes
5
replies
789
views
Creating a per sample file from multi-sample vcf
bcftools
SNV
SNP
vcftools
vcf
18 months ago by
tacrolimus
▴ 110
4
votes
1
reply
453
views
Pulling out "alts" from a multisample vcf by sample ID - bcftools syntax question
bcftools
vcf
20 months ago by
tacrolimus
▴ 110
3
votes
0
replies
453
views
Answer:
Answer: Pulling out "alts" from a multisample vcf by sample ID - bcftools syntax questio
20 months ago by
tacrolimus
▴ 110
0
votes
0
replies
294
views
Bioinformatic interrogation of non-coding variants in gVCFs
VCF
gVCF
non-coding
22 months ago by
tacrolimus
▴ 110
0
votes
0
replies
299
views
Best way of visualising genetic variation for publication in a gene with many exons
graphs
snv
lollipop
snp
Visualisation
23 months ago by
tacrolimus
▴ 110
0
votes
0
replies
668
views
Comment:
Comment: Count number of occurrences an annotation in a multisample vcf split into multip
23 months ago by
tacrolimus
▴ 110
4
votes
2
replies
668
views
Count number of occurrences an annotation in a multisample vcf split into multiple chunks
bcftools
vcf
annotation
23 months ago by
tacrolimus
▴ 110
0
votes
0
replies
873
views
Split Y-Axis of a manhattan plot in qqman (using R)
manhattan
R
genomics
23 months ago by
tacrolimus
▴ 110
0
votes
0
replies
1.1k
views
Comment:
C: Extract samples with alternative genotype from a multi-sample VCF
2.5 years ago by
tacrolimus
▴ 110
0
votes
0
replies
1.1k
views
Comment:
C: Extract samples with alternative genotype from a multi-sample VCF
2.5 years ago by
tacrolimus
▴ 110
0
votes
4
replies
1.1k
views
Extract samples with alternative genotype from a multi-sample VCF
vcf
bcftools
vep
updated 2.5 years ago by
abascalfederico
★ 1.2k • written 2.5 years ago by
tacrolimus
▴ 110
0
votes
0
replies
808
views
Adding SNP/Gene labels to a qqplot using qqman
qqman
qqplot
gwas
R
2.5 years ago by
tacrolimus
▴ 110
0
votes
0
replies
764
views
locuszoom on a HPC - LD could not be computed for SNP
locuszoom
HPC
bash
GWAS
2.6 years ago by
tacrolimus
▴ 110
0
votes
0
replies
1.5k
views
Comment:
C: Filtering large VCFs by allele freqency using bcftools split-vep function
2.6 years ago by
tacrolimus
▴ 110
1
vote
0
replies
1.3k
views
Comment:
C: Finding unique variants by sample ID in a multisample vcf
2.7 years ago by
tacrolimus
▴ 110
6
votes
2
replies
1.3k
views
Finding unique variants by sample ID in a multisample vcf
bcftools
vcf
SNP
vep
updated 2.7 years ago by
brunobsouzaa
▴ 810 • written 2.7 years ago by
tacrolimus
▴ 110
0
votes
0
replies
613
views
Leveraging phenotype data in rare variant and GWAS analysis
SNP
genome
phenotype
GWAS
rare variant
2.9 years ago by
tacrolimus
▴ 110
0
votes
0
replies
1.7k
views
Comment:
C: Faster filtering of vcfs using split-vep over filter_vep
updated 3.2 years ago by
finswimmer
16k • written 3.3 years ago by
tacrolimus
▴ 110
0
votes
1
reply
839
views
Answer:
A: Extract several columns from a VCF file
updated 3.2 years ago by
Ram
39k • written 3.3 years ago by
tacrolimus
▴ 110
0
votes
0
replies
839
views
Comment:
A: Extract several columns from a VCF file
3.3 years ago by
tacrolimus
▴ 110
1
vote
2
replies
1.7k
views
Faster filtering of vcfs using split-vep over filter_vep
VEP
bcftools
split-vep
vcf
3.3 years ago by
tacrolimus
▴ 110
3
votes
12
replies
959
views
BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a region
bcftools
3.3 years ago by
tacrolimus
▴ 110
0
votes
0
replies
959
views
Comment:
C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
3.3 years ago by
tacrolimus
▴ 110
0
votes
1
reply
959
views
Comment:
C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
3.3 years ago by
tacrolimus
▴ 110
0
votes
0
replies
959
views
Comment:
C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
3.3 years ago by
tacrolimus
▴ 110
0
votes
1
reply
959
views
Comment:
C: BCFTOOLS: One-liner to get individuals with more than one heterozygote call in a
3.3 years ago by
tacrolimus
▴ 110
0
votes
0
replies
883
views
Comment:
C: Creating a genotype matrix for BeviMed
3.4 years ago by
tacrolimus
▴ 110
3
votes
2
replies
883
views
Creating a genotype matrix for BeviMed
snp
genome
Bayesian
updated 2 days ago by
Ram
39k • written 3.4 years ago by
tacrolimus
▴ 110
2
votes
2
replies
1.5k
views
Filtering large VCFs by allele freqency using bcftools split-vep function
bcftools
vep
split-vep
3.6 years ago by
tacrolimus
▴ 110
0
votes
1
reply
1.9k
views
Comment:
C: Filtering multiple single person structural variant VCF files by type of SV
3.6 years ago by
tacrolimus
▴ 110
0
votes
1
reply
1.9k
views
Comment:
C: Filtering multiple single person structural variant VCF files by type of SV
3.6 years ago by
tacrolimus
▴ 110
3
votes
5
replies
1.9k
views
Filtering multiple single person structural variant VCF files by type of SV
structural variation
bcftools
vcf
unix
linux
3.6 years ago by
tacrolimus
▴ 110
0
votes
0
replies
1.2k
views
Comment:
C: Approach to structural variation analysis - case vs control
3.6 years ago by
tacrolimus
▴ 110
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