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641
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what does it mean when a plink bim file contains '*' as an allele
plink
4.0 years ago by curious ▴ 820
2
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4
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4.6k
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update-chr issues with PLINK 1.9
plink
updated 4.0 years ago by 20 • written 4.9 years ago by ▴ 820
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0
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872
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Comment: C: Is there a reason to limit dummy coding these alleles as 0 or 1 in this regressi
4.1 years ago by curious ▴ 820
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2
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872
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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
4.1 years ago by curious ▴ 820
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0
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830
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Comment: C: What is the smallest number of cases you can have in a GWAS before interpretatio
4.1 years ago by curious ▴ 820
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3
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830
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What is the smallest number of cases you can have in a GWAS before interpretation starts becoming troublesome
gwas
4.1 years ago by curious ▴ 820
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0
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1.8k
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Comment: C: logistic regression using HLA alllelic data
4.1 years ago by curious ▴ 820
7
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5
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1.5k
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Is there anyway to get a unix parallel command to write to standard output
unix
updated 4.1 years ago by ▴ 350 • written 4.1 years ago by ▴ 820
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0
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1.5k
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Comment: C: Is there anyway to get a unix parallel command to write to standard output
4.1 years ago by curious ▴ 820
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0
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760
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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
4.1 years ago by curious ▴ 820
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1
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1.2k
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Comment: C: How to do a multi-snp/haplotype based GWAS instead of a single snp GWAS in R?
4.1 years ago by curious ▴ 820
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1
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1.2k
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Comment: C: How to do a multi-snp/haplotype based GWAS instead of a single snp GWAS in R?
4.1 years ago by curious ▴ 820
0
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5
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1.2k
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How to do a multi-snp/haplotype based GWAS instead of a single snp GWAS in R?
gwas logistic glm
4.1 years ago by curious ▴ 820
0
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0
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1.9k
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Comment: C: bcftools subset by ids stored in a unix variable
4.1 years ago by curious ▴ 820
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2
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1.9k
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bcftools subset by ids stored in a unix variable
bcftools
updated 4.1 years ago by 164k • written 4.1 years ago by ▴ 820
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1
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1.7k
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Is there any wat to access the input of a snakemake rule in the output
snakemake
4.1 years ago by curious ▴ 820
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0
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1.7k
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Answer: A: Is there any wat to access the input of a snakemake rule in the output
4.1 years ago by curious ▴ 820
0
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0
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809
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Comment: C: Why are structural variants typically not tagged as well as SNPs?
4.2 years ago by curious ▴ 820
0
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0
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809
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Comment: C: Why are structural variants typically not tagged as well as SNPs?
4.2 years ago by curious ▴ 820
1
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3
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809
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Why are structural variants typically not tagged as well as SNPs?
wgs imputation structural variation
4.2 years ago by curious ▴ 820
0
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0
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813
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How is genotype imputation used in variant calling pipelines
variant calling 1000g
4.2 years ago by curious ▴ 820
0
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0
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3.4k
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Comment: C: How to do a Haplotype based GWAS?
4.2 years ago by curious ▴ 820
1
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2
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1.3k
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Is GWAS genotype QC to exclude samples with inbreeding coefficient typically applied to only autosomes?
gwas plink
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 820
1
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0
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1.3k
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Is it pretty common to have "reverse complemented alleles" when lifting over a vcf from hg19 to hg38?
liftover gatk picard
4.2 years ago by curious ▴ 820
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0
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2.6k
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Comment: C: Allele frequency calculation for genotype dosage value
4.2 years ago by curious ▴ 820
0
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0
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777
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Answer: A: Microarry (GSA) manifest file and CytoSNP-850K manifest file comparison
4.2 years ago by curious ▴ 820
1
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1
reply
1.1k
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Answer: A: Why different reference panels change the signal for a SNP?
4.3 years ago by curious ▴ 820
2
votes
1
reply
3.0k
views
What does it mean to calculate genomic control (lambda) at 10th percentile for GWAS
statistics
updated 4.3 years ago by 88k • written 4.4 years ago by ▴ 820
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0
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4.1k
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Comment: C: Switch ref/alt alleles vcf file
4.3 years ago by curious ▴ 820
0
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0
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1.2k
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How does beagle get phase for sites that are NOT in the reference panel
beagle phasing imputation
4.3 years ago by curious ▴ 820
2
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3
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1.3k
views
Does 1000 genomes have a flat file with allele frequencies for each site anywhere?
1000 genomes
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 820
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0
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1.3k
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Answer: A: Does 1000 genomes have a flat file with allele frequencies for each site anywher
4.3 years ago by curious ▴ 820
0
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1
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5.3k
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Comment: C: B allele frequency (BAF)
4.3 years ago by curious ▴ 820
2
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2
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731
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How is 1000 genomes so accessible when many other genotype/sequencing projects are fairly restricted in their access?
1000 genomes
updated 4.3 years ago by 148k • written 4.3 years ago by ▴ 820
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0
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1.8k
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Comment: C: What is the current standard for HLA allele typing prediction from SNP data?
4.3 years ago by curious ▴ 820
1
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0
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3.2k
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Comment: C: Post-imputation QC GWAS analysis
4.3 years ago by curious ▴ 820
2
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5
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1.5k
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Where does the 'simpleRepeat.txt' file from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ come from?
repeats golden path
4.3 years ago by curious ▴ 820
0
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0
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1.5k
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Answer: A: Where does the 'simpleRepeat.txt' file from http://hgdownload.cse.ucsc.edu/golde
4.3 years ago by curious ▴ 820
0
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0
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1.5k
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Comment: C: Where does the 'simpleRepeat.txt' file from http://hgdownload.cse.ucsc.edu/golde
4.3 years ago by curious ▴ 820
0
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0
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1.5k
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Comment: C: Where does the 'simpleRepeat.txt' file from http://hgdownload.cse.ucsc.edu/golde
4.3 years ago by curious ▴ 820
0
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1
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761
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Comment: C: Refrence datasets for imputation
4.3 years ago by curious ▴ 820
2
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0
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3.2k
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Answer: C: Post-imputation QC GWAS analysis
4.3 years ago by curious ▴ 820
0
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0
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576
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How many samples are too few for Hardy Weinberg equilibrium test?
gwas
4.3 years ago by curious ▴ 820
0
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1
reply
1.1k
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Comment: C: Can variant callers distinguish between a snp and the end of an indel?
4.3 years ago by curious ▴ 820
0
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1
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1.1k
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Comment: C: Can variant callers distinguish between a snp and the end of an indel?
4.3 years ago by curious ▴ 820
0
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0
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1.1k
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Comment: C: Can variant callers distinguish between a snp and the end of an indel?
4.3 years ago by curious ▴ 820
3
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6
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1.1k
views
Can variant callers distinguish between a snp and the end of an indel?
1000 genomes vcf variant calling
updated 4.3 years ago by 44k • written 4.3 years ago by ▴ 820
0
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0
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2.8k
views
Comment: C: Differentially expressed genes machine learning classifer
4.3 years ago by curious ▴ 820
1
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1
reply
2.8k
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Comment: C: Differentially expressed genes machine learning classifer
4.3 years ago by curious ▴ 820
0
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0
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4.1k
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Answer: A: IDAT to VCF conversion
4.3 years ago by curious ▴ 820
300 results • Page 3 of 6
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