Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
1
vote
3
replies
727
views
What is the smallest number of cases you can have in a GWAS before interpretation starts becoming troublesome
gwas
3.5 years ago by curious ▴ 750
7
votes
5
replies
1.3k
views
Is there anyway to get a unix parallel command to write to standard output
unix
updated 3.5 years ago by ▴ 310 • written 3.5 years ago by ▴ 750
0
votes
0
replies
683
views
Is this the correct notation for the logistic regression I am trying to describe? I am very new to statistics notation and LaTeX
latex logistic regression association
3.5 years ago by curious ▴ 750
0
votes
5
replies
1.0k
views
How to do a multi-snp/haplotype based GWAS instead of a single snp GWAS in R?
gwas logistic glm
3.5 years ago by curious ▴ 750
0
votes
2
replies
1.7k
views
bcftools subset by ids stored in a unix variable
bcftools
updated 3.5 years ago by 161k • written 3.5 years ago by ▴ 750
0
votes
1
reply
1.6k
views
Is there any wat to access the input of a snakemake rule in the output
snakemake
3.5 years ago by curious ▴ 750
1
vote
3
replies
729
views
Why are structural variants typically not tagged as well as SNPs?
wgs imputation structural variation
3.6 years ago by curious ▴ 750
0
votes
0
replies
738
views
How is genotype imputation used in variant calling pipelines
variant calling 1000g
3.6 years ago by curious ▴ 750
1
vote
2
replies
1.2k
views
Is GWAS genotype QC to exclude samples with inbreeding coefficient typically applied to only autosomes?
gwas plink
updated 3.6 years ago by 20 • written 3.7 years ago by ▴ 750
1
vote
0
replies
1.2k
views
Is it pretty common to have "reverse complemented alleles" when lifting over a vcf from hg19 to hg38?
liftover gatk picard
3.6 years ago by curious ▴ 750
2
votes
1
reply
2.8k
views
What does it mean to calculate genomic control (lambda) at 10th percentile for GWAS
statistics
updated 3.7 years ago by 88k • written 3.8 years ago by ▴ 750
0
votes
0
replies
1.1k
views
How does beagle get phase for sites that are NOT in the reference panel
beagle phasing imputation
3.7 years ago by curious ▴ 750
2
votes
3
replies
1.2k
views
Does 1000 genomes have a flat file with allele frequencies for each site anywhere?
1000 genomes
updated 3.7 years ago by ★ 3.8k • written 3.7 years ago by ▴ 750
2
votes
2
replies
631
views
How is 1000 genomes so accessible when many other genotype/sequencing projects are fairly restricted in their access?
1000 genomes
updated 3.7 years ago by 142k • written 3.7 years ago by ▴ 750
2
votes
5
replies
1.3k
views
Where does the 'simpleRepeat.txt' file from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ come from?
repeats golden path
3.7 years ago by curious ▴ 750
0
votes
0
replies
533
views
How many samples are too few for Hardy Weinberg equilibrium test?
gwas
3.7 years ago by curious ▴ 750
3
votes
6
replies
935
views
Can variant callers distinguish between a snp and the end of an indel?
1000 genomes vcf variant calling
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 750
0
votes
0
replies
789
views
Lifting over results in coordinates that do not agree with what the rsid suggests the coordinates should be?
liftover hla
3.8 years ago by curious ▴ 750
1
vote
5
replies
2.4k
views
filter VCF based on info field that has a key but no value
bcftools vcf
updated 3.8 years ago by • 0 • written 4.3 years ago by ▴ 750
0
votes
0
replies
1.2k
views
How does imputation software calculate haploid alternate allele dosage from posterior probabilities for genotypes?
impuation
3.8 years ago by curious ▴ 750
0
votes
2
replies
967
views
Simulating whole gene deletions for tuning a WES based CNV calling approach?
WES
3.8 years ago by curious ▴ 750
0
votes
0
replies
886
views
Lifting over and harmonizing a plink file so major allele is forward on hg19?
plink strand liftover
3.9 years ago by curious ▴ 750
0
votes
0
replies
585
views
Using only non-reference homozygous sites to evaluate SNP array concordance?
snp array
3.9 years ago by curious ▴ 750
0
votes
2
replies
879
views
Setting major allele in plink to plus strand of reference?
plink
3.9 years ago by curious ▴ 750
3
votes
2
replies
3.7k
views
Possible to add `chr` prefix to each chromosome in PLINK?
plink
updated 3.9 years ago by 10k • written 3.9 years ago by ▴ 750
0
votes
1
reply
1.8k
views
How to add a flag to the INFO column of a vcf with pysam?
bcf vcf pysam
3.9 years ago by curious ▴ 750
0
votes
2
replies
2.6k
views
Is there any way to make samtools tabix go faster?
tabix vcf bcf samtools
3.9 years ago by curious ▴ 750
3
votes
9
replies
1.9k
views
Fastest was to sort a 340 gb BCF by chromosome and position?
bcf bcftools
3.9 years ago by curious ▴ 750
3
votes
2
replies
5.9k
views
bcftools view -r seems to be getting sites outside of the region I designate?
bcftools vcf bcf
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 750
1
vote
3
replies
862
views
Fastest way to switch out sites on one BCF for sites in another BCF?
bcftools bcf vcf
4.0 years ago by curious ▴ 750
3
votes
2
replies
2.4k
views
Speed of merging multiple bcfs with bcftools compared to PLINK?
bcftools plink
4.0 years ago by curious ▴ 750
3
votes
4
replies
4.4k
views
Flipping every REF/ALT and corresponsing genotypes of every single indel in a VCF.
bcftools oxford plink
4.0 years ago by curious ▴ 750
2
votes
3
replies
808
views
Using bcftools merge on the output of multiple process substitution? (somewhat a linux question)
linux
4.0 years ago by curious ▴ 750
1
vote
4
replies
1.6k
views
Doing an operation on one huge VCF, use Python or would C be faster (somewhat niave bcftools/computer science question)
python bcftools c vcf
4.0 years ago by curious ▴ 750
0
votes
0
replies
674
views
Removing rare variants from SNP array before imputation then putting them back in after imputation?
imputation snp array
4.0 years ago by curious ▴ 750
0
votes
0
replies
676
views
what does: "Allele mismatch Ref:G/T" mean in the QC report from the michigan imputation server?
imputation
4.0 years ago by curious ▴ 750
0
votes
0
replies
741
views
Trying to figure out coordinates for long range LD regions on build 38 for flashpca
flashpca ld
4.1 years ago by curious ▴ 750
1
vote
3
replies
647
views
simple question about insertion standards in vcf 4.2
vcf specificaiton
updated 4.1 years ago by 10k • written 4.1 years ago by ▴ 750
0
votes
0
replies
701
views
**Is nonreference discordance just (Number of ALT mismatches/Number of ALT matches)*100?**
vcf-compare vcf
4.1 years ago by curious ▴ 750
5
votes
4
replies
6.0k
views
VCF to BCF conversion with bcftools?
bcftools
updated 4.2 years ago by 161k • written 4.2 years ago by ▴ 750
11
votes
5
replies
10k
views
bcftools selest sites with FILTER "PASS" or "."
bcftools
updated 4.2 years ago by 161k • written 4.2 years ago by ▴ 750
1
vote
3
replies
591
views
Standard approach for telling if sites were removed during calling due to poor quality or non-variant?
gatk vcf
4.2 years ago by curious ▴ 750
0
votes
0
replies
693
views
Standard cutoffs for call-rate when filtering a VCF?
gatk vcf
4.2 years ago by curious ▴ 750
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk variant calling sureselect
updated 9 months ago by • 0 • written 4.2 years ago by ▴ 750
0
votes
0
replies
798
views
Is it a convention for displaying human males in VCF as homozygous diploid?
vcf diploid
4.2 years ago by curious ▴ 750
0
votes
4
replies
1.1k
views
Good quality control metrics to look out for when someone gives you BAMs
bam qc
4.3 years ago by curious ▴ 750
1
vote
2
replies
1.1k
views
Genetic map for chromosome X that shows recombination rates?
shapeit phasing
updated 4.3 years ago by 88k • written 4.3 years ago by ▴ 750
0
votes
0
replies
890
views
Trouble understanding Eagle2 phasing software "--allowRefAltSwap" flag
eagle phasing
4.3 years ago by curious ▴ 750
0
votes
2
replies
1.0k
views
A2 different between PLINK .bim file and .frq file?
plink
updated 4.3 years ago by 10k • written 4.3 years ago by ▴ 750
0
votes
0
replies
1.3k
views
Evaluating switch error rate when phasing with Eagle2?
phasing gwas eagle beagle
4.3 years ago by curious ▴ 750
113 results • Page 2 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