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Answer: Answer: New datasets for ancestry estimation and imputation?
2.5 years ago by curious ▴ 750
1
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1
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766
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inner merge vcfs in one step?
bcftools
updated 2.5 years ago by 161k • written 2.5 years ago by ▴ 750
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3.3k
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Comment: Comment: Applying Machine Learning on vcf file
2.5 years ago by curious ▴ 750
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477
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Is it possible to report the allele frequency of integer copy numbers >= 3?
cn.mops cnv
2.6 years ago by curious ▴ 750
2
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1
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566
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how to get exon regions for this gene w/ build 19 coordinates
bed
updated 2.7 years ago by 142k • written 2.7 years ago by ▴ 750
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2.2k
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Answer: Answer: Snakemake bwa mem
2.7 years ago by curious ▴ 750
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971
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Answer: Answer: What is the best software for "phasing" in human population genomics with trio f
2.7 years ago by curious ▴ 750
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1.3k
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Comment: Comment: is local ancestry inference typically always run w/ array genotypes instead of
2.7 years ago by curious ▴ 750
1
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4
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1.3k
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is local ancestry inference typically always run w/ array genotypes instead of imputed genotypes?
ancestry
updated 2.7 years ago by 4.2k • written 2.7 years ago by ▴ 750
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895
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Comment: Comment: RFMix v2 - ancestry per individual marker
2.7 years ago by curious ▴ 750
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7
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2.3k
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How do I log into this ftp server and look around?
ftp
updated 2.7 years ago by ★ 27k • written 2.7 years ago by ▴ 750
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2.3k
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Comment: Comment: How do I log into this ftp server and look around?
2.7 years ago by curious ▴ 750
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2
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2.3k
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Comment: Comment: How do I log into this ftp server and look around?
2.7 years ago by curious ▴ 750
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0
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3.0k
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Comment: Comment: Highly used R packages with no Python equivalent
2.7 years ago by curious ▴ 750
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0
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491
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is it possible to subset samples and reheader a vcf in a single step?
bcftools
2.8 years ago by curious ▴ 750
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0
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773
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can you use LD scores from build 37 reference to get LD score intercept on build 38 summary stats?
ld regression score
2.8 years ago by curious ▴ 750
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2
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5.8k
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Comment: Comment: sorting a multi-sample (genotype) vcf file
2.8 years ago by curious ▴ 750
4
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2
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1.6k
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You can't just liftover from one build to another using only coordinates correct?
liftover
updated 2.9 years ago by ▴ 10 • written 3.3 years ago by ▴ 750
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1.8k
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Comment: Comment: what pihat cutoffs from plink --genome are 3rd degree relative
2.9 years ago by curious ▴ 750
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1
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1.8k
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what pihat cutoffs from plink --genome are 3rd degree relative
related ibd plink
2.9 years ago by curious ▴ 750
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1
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1.1k
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Comment: Comment: Make map file with recombination rate using plink?
2.9 years ago by curious ▴ 750
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3
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1.1k
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Make map file with recombination rate using plink?
germline plink
updated 2.9 years ago by 2.8k • written 2.9 years ago by ▴ 750
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788
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Comment: Comment: how to identify haplotypes and its frequency based SNP genotyping data?
3.0 years ago by curious ▴ 750
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0
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580
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Comment: Comment: Does this output indicate my bam is paired end?
3.0 years ago by curious ▴ 750
1
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2
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580
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Does this output indicate my bam is paired end?
samtools
3.0 years ago by curious ▴ 750
2
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0
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2.3k
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Answer: Answer: How to connect HLA alleles with rsID?
3.0 years ago by curious ▴ 750
0
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1
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993
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Comment: Comment: Could someone help me check what genomic position is this variant nomenclature r
3.0 years ago by curious ▴ 750
1
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5
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993
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Could someone help me check what genomic position is this variant nomenclature referring to ?
nomeclature
updated 3.0 years ago by 21k • written 3.0 years ago by ▴ 750
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3.2k
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Answer: Answer: how to run linux code in python
3.0 years ago by curious ▴ 750
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0
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1.3k
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Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.0 years ago by curious ▴ 750
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1
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1.3k
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Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.0 years ago by curious ▴ 750
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4
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1.3k
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quick way to get samples that are NOT homozygous reference for a given record using bcftools?
bcftools
3.0 years ago by curious ▴ 750
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0
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693
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Does a smaller value of F from PLINK --het represent higher heterozygosity?
plink
3.1 years ago by curious ▴ 750
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461
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is the absolute value of `plink2.eigenvec.var` from `plink2 --pca biallelic-var-wts approx` a measure of how much each SNP drives PCS?
plink
3.1 years ago by curious ▴ 750
0
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1
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745
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Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 2.3 years ago by ▴ 180 • written 3.1 years ago by ▴ 750
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0
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881
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Comment: C: STAR alignment loop segmentation fualt (core dumped)
3.2 years ago by curious ▴ 750
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0
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1.3k
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Comment: C: How do I organize snakemake when not all jobs successfully output files from pre
3.2 years ago by curious ▴ 750
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0
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756
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Answer: A: Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
3.2 years ago by curious ▴ 750
3
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3
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915
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how to use unix tools to convert VCF genotypes like '1|1' to this '2'
bcftools unix
updated 10 months ago by 43k • written 3.2 years ago by ▴ 750
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0
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915
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Comment: C: how to use unix tools to convert VCF genotypes like '1|1' to this '2'
3.2 years ago by curious ▴ 750
1
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1
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651
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"SNP" record in vcf looks like this: 6:28035427:GTA:ATA ?
vcf
3.2 years ago by curious ▴ 750
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2.2k
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Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
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0
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1.2k
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Is this an OK approach for lifting over a mixture of b36 & b37 to b38 variants using rsids only?
liftover
3.3 years ago by curious ▴ 750
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1
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2.2k
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Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
1
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1
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2.2k
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Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
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0
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586
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what does it mean when a plink bim file contains '*' as an allele
plink
3.3 years ago by curious ▴ 750
2
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4
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3.9k
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update-chr issues with PLINK 1.9
plink
updated 3.4 years ago by 20 • written 4.2 years ago by ▴ 750
0
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0
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780
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Comment: C: Is there a reason to limit dummy coding these alleles as 0 or 1 in this regressi
3.4 years ago by curious ▴ 750
1
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2
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780
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Is there a reason to limit dummy coding these alleles as 0 or 1 in this regression model example, instead of allowing values of 0,1,or 2?
logistic regression gwas
3.4 years ago by curious ▴ 750
0
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0
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713
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Comment: C: What is the smallest number of cases you can have in a GWAS before interpretatio
3.4 years ago by curious ▴ 750
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