Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
0
votes
5
replies
376
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 11 days ago by 10k • written 12 days ago by ▴ 750
0
votes
2
replies
238
views
Can't figure out plink --sample-diff
plink
5 weeks ago by curious ▴ 750
3
votes
2
replies
394
views
Why do these two variants appear to result in the same amino acid change when annotated by snpeff, but are annotated differently in clinvar
clinvar
3 months ago by curious ▴ 750
1
vote
1
reply
304
views
Is there a way to map Medgen # to OMIM # programmatically?
medgen omim
updated 4 months ago by 161k • written 4 months ago by ▴ 750
0
votes
1
reply
414
views
Where do these snpeff annotation come from?
snpeff
updated 5 months ago by 100k • written 5 months ago by ▴ 750
0
votes
4
replies
1.2k
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 7 months ago by 10k • written 8 months ago by ▴ 750
1
vote
1
reply
447
views
bcftools update ID keeping only string after ';'
bcftools
updated 8 months ago by 161k • written 8 months ago by ▴ 750
0
votes
5
replies
636
views
Is this a valid allele in a vcf?
vcf
updated 9 months ago by 43k • written 9 months ago by ▴ 750
0
votes
6
replies
676
views
Is it possible to interpret HGVS without transcript version number?
hgvs
updated 9 months ago by ★ 1.2k • written 9 months ago by ▴ 750
0
votes
2
replies
394
views
jannovar download problem
jannovar
9 months ago by curious ▴ 750
2
votes
2
replies
527
views
Why does this stop gained result in a longer protein than the canonical version
ensembl
updated 10 months ago by 43k • written 10 months ago by ▴ 750
2
votes
2
replies
1.5k
views
Download VCF for dbsnp 156?
dbsnp
updated 10 months ago by 142k • written 10 months ago by ▴ 750
0
votes
1
reply
459
views
Any way to get bcftools to query up to but not including the last site given in a region query
bcftools
updated 10 months ago by 161k • written 10 months ago by ▴ 750
4
votes
3
replies
1.0k
views
What does canonical transcript mean in the context of VEP
vep
updated 11 months ago by 4.2k • written 11 months ago by ▴ 750
1
vote
4
replies
703
views
viewing hgvs in genome data viewer
ncbi hgvs clinvar
12 months ago by curious ▴ 750
0
votes
0
replies
311
views
Trying to understand the difference between between these two HGVS
hgvs
15 months ago by curious ▴ 750
2
votes
2
replies
786
views
drop duplicate insertion deletions in VCF at same position while keeping one
bcftools
15 months ago by curious ▴ 750
2
votes
1
reply
876
views
In GWAS what is the point of regressing a quantitative phenotype on covariates first and taking the residuals?
gwas
updated 16 months ago by 3.9k • written 16 months ago by ▴ 750
1
vote
1
reply
499
views
calculating the allele frequency of a gene deletion and duplication
cnv
updated 16 months ago by ★ 2.9k • written 16 months ago by ▴ 750
5
votes
11
replies
2.2k
views
fast way to get last position in a large indexed VCF?
bcftools
updated 20 months ago by 100k • written 20 months ago by ▴ 750
0
votes
3
replies
816
views
is it possible to calculate MAF from DS instead of GT when using bcftools +fill-tags?
bcftools
20 months ago by curious ▴ 750
1
vote
0
replies
411
views
Does genomic control have a valid interpretation when there are no genome-wide significant hits
genomic control statistics
22 months ago by curious ▴ 750
0
votes
0
replies
387
views
am I understanding scaled CADD scores correct?
cadd
24 months ago by curious ▴ 750
2
votes
1
reply
505
views
Using snpsift to filter VCF by sample
snpsift
updated 2.0 years ago by 161k • written 2.0 years ago by ▴ 750
0
votes
0
replies
392
views
Does larger standardized PRS value always means higher risk?
prs
2.1 years ago by curious ▴ 750
0
votes
0
replies
559
views
Converting observed heritability to liability scale, how to get standard error?
hertiability greml ldsc
2.2 years ago by curious ▴ 750
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
768
views
inner merge vcfs in one step?
bcftools
updated 2.6 years ago by 161k • written 2.6 years ago by ▴ 750
0
votes
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
569
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
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
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
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
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
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
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
1
vote
2
replies
582
views
Does this output indicate my bam is paired end?
samtools
3.0 years ago by curious ▴ 750
1
vote
5
replies
997
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
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
462
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
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
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
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
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
2
votes
4
replies
3.9k
views
update-chr issues with PLINK 1.9
plink
updated 3.4 years ago by 20 • written 4.3 years ago by ▴ 750
1
vote
2
replies
784
views
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
3.5 years ago by curious ▴ 750
113 results • Page 1 of 3
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6