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4
votes
1
reply
1.0k
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GATK site filtering: when should I use VQSR or hard filtering?
VQSR GATK
updated 5 months ago by • 0 • written 3.7 years ago by ▴ 270
0
votes
0
replies
744
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Comment: Comment: Is ComBat not able to to handle only two batches? What are good alternatives?
10 months ago by samuelandjw ▴ 270
2
votes
3
replies
744
views
Is ComBat not able to to handle only two batches? What are good alternatives?
ComBat batch correction
10 months ago by samuelandjw ▴ 270
0
votes
0
replies
512
views
Finding a list of heritable traits using GCTA
complex heritability traits GCTA
3.0 years ago by samuelandjw ▴ 270
2
votes
1
reply
776
views
Should we include genotype as covariates when performing EWAS?
methylation EWAS DNA
updated 2.5 years ago by 45k • written 3.1 years ago by ▴ 270
2
votes
1
reply
725
views
What are the general strategies in assessing new differentially methylation positions obtained from EWAS?
methylation EWAS DNA
updated 2.5 years ago by 45k • written 3.1 years ago by ▴ 270
4
votes
1
reply
725
views
Is it okay to map reads from WES designed for GRCh37 to GRCh38?
exome whole sequencing
updated 3.1 years ago by 166k • written 3.1 years ago by ▴ 270
0
votes
0
replies
577
views
How to get list of blood-expressed Fantom 5 enhancers?
fantom5
updated 3.1 years ago by 45k • written 3.1 years ago by ▴ 270
0
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1
reply
1.1k
views
Comment: Comment: How to access the NCBI Molecular QTL Browser?
3.1 years ago by samuelandjw ▴ 270
1
vote
3
replies
1.1k
views
How to access the NCBI Molecular QTL Browser?
QTL
updated 3.1 years ago by 152k • written 3.1 years ago by ▴ 270
0
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0
replies
9.1k
views
Comment: Comment: Any FastQC alternative
3.2 years ago by samuelandjw ▴ 270
0
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0
replies
424
views
How to group EWAS traits like GWAS catalog does?
GWAS EWAS
3.2 years ago by samuelandjw ▴ 270
3
votes
1
reply
759
views
reference request: list of DNA methylation sites with consistent methylation levels across individuals in blood
methylation DNA
updated 3.3 years ago by ★ 3.1k • written 3.3 years ago by ▴ 270
0
votes
0
replies
1.3k
views
Answer: Answer: Unable to install dplyr on Fedora 35
3.3 years ago by samuelandjw ▴ 270
1
vote
1
reply
726
views
EWAS: should DNA methylation level be the independent variable or dependent variable?
DNA EWAS methylation
updated 2.8 years ago by • 0 • written 3.5 years ago by ▴ 270
0
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0
replies
2.0k
views
Comment: Comment: Best practice for running GATK VQSR on X chromosome
3.6 years ago by samuelandjw ▴ 270
1
vote
1
reply
771
views
Should we trust genotypes called in simple tandem repeat regions?
sequencing GATK WGS WES
updated 3.6 years ago by 102k • written 3.6 years ago by ▴ 270
0
votes
0
replies
875
views
Comment: Comment: What is the largest freely available dataset of WGS samples?
3.6 years ago by samuelandjw ▴ 270
1
vote
0
replies
2.5k
views
Answer: Answer: How to subset vcf by sample and write?
3.9 years ago by samuelandjw ▴ 270
1
vote
0
replies
969
views
Comment: Comment: GATK VQSR for human WGS
3.9 years ago by samuelandjw ▴ 270
0
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0
replies
2.5k
views
Comment: Comment: Error in plot-vcfstats
3.9 years ago by samuelandjw ▴ 270
2
votes
0
replies
2.0k
views
Comment: Comment: Using vcftools and got Error: Unknown option: --max-missing
3.9 years ago by samuelandjw ▴ 270
0
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1
reply
8.0k
views
Comment: Comment: plot-vcfstats
3.9 years ago by samuelandjw ▴ 270
2
votes
1
reply
8.0k
views
Answer: Answer: plot-vcfstats
3.9 years ago by samuelandjw ▴ 270
0
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0
replies
2.0k
views
Comment: Comment: Best practice for running GATK VQSR on X chromosome
3.9 years ago by samuelandjw ▴ 270
0
votes
4
replies
2.0k
views
Best practice for running GATK VQSR on X chromosome
WGS GATK WES
3.6 years ago by samuelandjw ▴ 270
0
votes
1
reply
3.6k
views
Comment: Comment: Why is WGS/WES depth of Y chromosome highly variable?
3.9 years ago by samuelandjw ▴ 270
1
vote
0
replies
3.6k
views
Comment: Comment: Why is WGS/WES depth of Y chromosome highly variable?
3.9 years ago by samuelandjw ▴ 270
11
votes
13
replies
3.6k
views
Why is WGS/WES depth of Y chromosome highly variable?
chromosome-Y whole-genome-sequencing
updated 2.5 years ago by 45k • written 3.9 years ago by ▴ 270
0
votes
1
reply
3.6k
views
Comment: Comment: Why is WGS/WES depth of Y chromosome highly variable?
3.9 years ago by samuelandjw ▴ 270
0
votes
0
replies
7.9k
views
Comment: Comment: GATK genomicsDBimport intervals for WGS
3.9 years ago by samuelandjw ▴ 270
1
vote
0
replies
4.2k
views
Comment: Comment: Why is VCFtools excluding invariable sites?
4.2 years ago by samuelandjw ▴ 270
0
votes
0
replies
7.8k
views
Comment: Comment: plotting PCA PLINK eigenvec output in R
4.2 years ago by samuelandjw ▴ 270
3
votes
1
reply
7.8k
views
Answer: Answer: plotting PCA PLINK eigenvec output in R
4.2 years ago by samuelandjw ▴ 270
0
votes
0
replies
783
views
Convert spanning deletions called by GATK back to regular indels
GATK sequencing
4.6 years ago by samuelandjw ▴ 270
0
votes
0
replies
2.5k
views
Answer: A: How do I plot RFMix results?
4.7 years ago by samuelandjw ▴ 270
0
votes
0
replies
10k
views
Comment: C: bwa mem hard clipping
5.5 years ago by samuelandjw ▴ 270
0
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0
replies
25k
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Comment: C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
5.6 years ago by samuelandjw ▴ 270
0
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0
replies
2.2k
views
Comment: C: meaning of Q_bias ADMIXTURE bootstrap
5.8 years ago by samuelandjw ▴ 270
1
vote
2
replies
2.2k
views
meaning of Q_bias ADMIXTURE bootstrap
admixture population ancestry
updated 5.8 years ago by • 0 • written 6.3 years ago by ▴ 270
0
votes
1
reply
1.2k
views
refine population phased haplotypes by pedigree
phasing genotype pedigree population
updated 5.9 years ago by • 0 • written 6.3 years ago by ▴ 270
4
votes
0
replies
2.1k
views
Answer: A: ADMIXTURE haploid mode does not converge
6.3 years ago by samuelandjw ▴ 270
4
votes
1
reply
2.1k
views
ADMIXTURE haploid mode does not converge
admixture population
updated 2.5 years ago by 45k • written 6.3 years ago by ▴ 270
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