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3
votes
4
replies
1.1k
views
keep samples that carry non-reference allele in list of variants snpeff/snpsift
snpeff snpsift bcftools
2.3 years ago by curious ▴ 750
0
votes
1
reply
733
views
subset vcf to keep only samples heterozygous or homozygous for the alternate allele of a given variant
bcftools
updated 2.3 years ago by ★ 1.1k • written 2.3 years ago by ▴ 750
1
vote
1
reply
1.4k
views
Answer: Answer: Haploview.jar
2.4 years ago by curious ▴ 750
0
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0
replies
3.3k
views
Comment: Comment: Applying Machine Learning on vcf file
2.5 years ago by curious ▴ 750
1
vote
0
replies
1.4k
views
Answer: Answer: New datasets for ancestry estimation and imputation?
2.6 years ago by curious ▴ 750
1
vote
1
reply
772
views
inner merge vcfs in one step?
bcftools
updated 2.6 years ago by 161k • written 2.6 years ago by ▴ 750
0
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1
reply
3.3k
views
Comment: Comment: Applying Machine Learning on vcf file
2.6 years ago by curious ▴ 750
0
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0
replies
481
views
Is it possible to report the allele frequency of integer copy numbers >= 3?
cn.mops cnv
2.7 years ago by curious ▴ 750
2
votes
1
reply
570
views
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
1
vote
0
replies
2.2k
views
Answer: Answer: Snakemake bwa mem
2.7 years ago by curious ▴ 750
0
votes
0
replies
983
views
Answer: Answer: What is the best software for "phasing" in human population genomics with trio f
2.7 years ago by curious ▴ 750
0
votes
2
replies
1.3k
views
Comment: Comment: is local ancestry inference typically always run w/ array genotypes instead of
2.8 years ago by curious ▴ 750
1
vote
4
replies
1.3k
views
is local ancestry inference typically always run w/ array genotypes instead of imputed genotypes?
ancestry
updated 2.8 years ago by 4.2k • written 2.8 years ago by ▴ 750
0
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0
replies
901
views
Comment: Comment: RFMix v2 - ancestry per individual marker
2.8 years ago by curious ▴ 750
2
votes
7
replies
2.3k
views
How do I log into this ftp server and look around?
ftp
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 750
0
votes
0
replies
2.3k
views
Comment: Comment: How do I log into this ftp server and look around?
2.8 years ago by curious ▴ 750
0
votes
2
replies
2.3k
views
Comment: Comment: How do I log into this ftp server and look around?
2.8 years ago by curious ▴ 750
0
votes
0
replies
3.0k
views
Comment: Comment: Highly used R packages with no Python equivalent
2.8 years ago by curious ▴ 750
0
votes
0
replies
495
views
is it possible to subset samples and reheader a vcf in a single step?
bcftools
2.8 years ago by curious ▴ 750
0
votes
0
replies
780
views
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
0
votes
2
replies
5.9k
views
Comment: Comment: sorting a multi-sample (genotype) vcf file
2.9 years ago by curious ▴ 750
4
votes
2
replies
1.6k
views
You can't just liftover from one build to another using only coordinates correct?
liftover
updated 2.9 years ago by ▴ 10 • written 3.4 years ago by ▴ 750
0
votes
0
replies
1.9k
views
Comment: Comment: what pihat cutoffs from plink --genome are 3rd degree relative
3.0 years ago by curious ▴ 750
0
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1
reply
1.9k
views
what pihat cutoffs from plink --genome are 3rd degree relative
related ibd plink
3.0 years ago by curious ▴ 750
0
votes
1
reply
1.1k
views
Comment: Comment: Make map file with recombination rate using plink?
3.0 years ago by curious ▴ 750
0
votes
3
replies
1.1k
views
Make map file with recombination rate using plink?
germline plink
updated 3.0 years ago by 2.8k • written 3.0 years ago by ▴ 750
0
votes
0
replies
802
views
Comment: Comment: how to identify haplotypes and its frequency based SNP genotyping data?
3.0 years ago by curious ▴ 750
0
votes
0
replies
583
views
Comment: Comment: Does this output indicate my bam is paired end?
3.1 years ago by curious ▴ 750
1
vote
2
replies
583
views
Does this output indicate my bam is paired end?
samtools
3.1 years ago by curious ▴ 750
2
votes
0
replies
2.3k
views
Answer: Answer: How to connect HLA alleles with rsID?
3.1 years ago by curious ▴ 750
0
votes
1
reply
999
views
Comment: Comment: Could someone help me check what genomic position is this variant nomenclature r
3.1 years ago by curious ▴ 750
1
vote
5
replies
999
views
Could someone help me check what genomic position is this variant nomenclature referring to ?
nomeclature
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 750
0
votes
0
replies
3.3k
views
Answer: Answer: how to run linux code in python
3.1 years ago by curious ▴ 750
0
votes
0
replies
1.3k
views
Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.1 years ago by curious ▴ 750
0
votes
1
reply
1.3k
views
Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.1 years ago by curious ▴ 750
0
votes
4
replies
1.3k
views
quick way to get samples that are NOT homozygous reference for a given record using bcftools?
bcftools
3.1 years ago by curious ▴ 750
0
votes
0
replies
700
views
Does a smaller value of F from PLINK --het represent higher heterozygosity?
plink
3.1 years ago by curious ▴ 750
0
votes
0
replies
463
views
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
votes
1
reply
756
views
Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 2.3 years ago by ▴ 180 • written 3.2 years ago by ▴ 750
0
votes
0
replies
889
views
Comment: C: STAR alignment loop segmentation fualt (core dumped)
3.2 years ago by curious ▴ 750
0
votes
0
replies
1.3k
views
Comment: C: How do I organize snakemake when not all jobs successfully output files from pre
3.2 years ago by curious ▴ 750
0
votes
0
replies
764
views
Answer: A: Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
3.2 years ago by curious ▴ 750
3
votes
3
replies
921
views
how to use unix tools to convert VCF genotypes like '1|1' to this '2'
bcftools unix
updated 11 months ago by 43k • written 3.2 years ago by ▴ 750
0
votes
0
replies
921
views
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
vote
1
reply
656
views
"SNP" record in vcf looks like this: 6:28035427:GTA:ATA ?
vcf
3.3 years ago by curious ▴ 750
0
votes
0
replies
2.2k
views
Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
0
votes
0
replies
1.2k
views
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
0
votes
1
reply
2.2k
views
Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
1
vote
1
reply
2.2k
views
Comment: C: Merging WGS SNP array data
3.3 years ago by curious ▴ 750
0
votes
0
replies
588
views
what does it mean when a plink bim file contains '*' as an allele
plink
3.4 years ago by curious ▴ 750
299 results • Page 2 of 6
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