User user438383

5 votes

How is the GT field in a VCF file defined?

answered Sep 14, 2020 at 10:23

4 votes

Accepted

What should be the numbers in the fastSTRUCTURE file?

answered Sep 23, 2020 at 12:52

4 votes

Accepted

How to convert a BAM file into a VCF file

answered Feb 17, 2022 at 12:00

3 votes

what are the nodes and edges values in gene regulatory networks?

answered Jan 20, 2022 at 10:36

3 votes

Accepted

Extracting a column from a vcf file

answered Jan 26, 2022 at 15:32

3 votes

Accepted

Question about public availability of human SNP dataset with country of origin

answered Mar 12, 2021 at 7:02

3 votes

Accepted

Renaming samples in vcf file

answered Jun 9, 2021 at 14:20

3 votes

Are variant calling files personally identifiable information?

answered Jun 29, 2021 at 11:06

3 votes

Accepted

Is there any database about the abundance of proteins in urine of healthy patients?

answered Sep 23, 2021 at 9:02

3 votes

Accepted

Tutorials on phasing and imputing low-coverage sequencing data

answered Dec 27, 2021 at 16:59

3 votes

Accepted

Download or create VCF from Human Genome Diversity Project (HGDP)

answered Jul 27, 2020 at 13:53

3 votes

Accepted

How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

answered Feb 16, 2020 at 11:34

3 votes

Imputing small region of the genome

answered Apr 27, 2022 at 9:59

3 votes

BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code

answered Jun 30, 2022 at 13:55

3 votes

Accepted

Problem with samtools command with a final hyphen

answered Mar 24 at 11:13

2 votes

Reference for the statistical methodology used in joint genotype calling

answered Dec 24, 2022 at 12:38

2 votes

Accepted

correlation between imputed genotype and true genotype

answered Sep 7, 2022 at 17:35

2 votes

Accepted

Where can I download 30x 1000 genomes cram files?

answered Sep 9, 2022 at 12:16

2 votes

Q: What analyses can I perform with a completely phased genome assembly?

answered Feb 17, 2020 at 11:52

2 votes

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

answered Jul 27, 2020 at 13:43

2 votes

Find overlap between VCF files

answered May 31, 2019 at 23:01

2 votes

plink: --update-name vs. editing the BIM

answered Aug 25, 2020 at 7:22

2 votes

Inheritance annotation for nsSNPs

answered Sep 10, 2020 at 13:36

2 votes

How can I subset WGS data to the level of WES variants?

answered Nov 16, 2020 at 11:18

2 votes

Summing up one column entries for each sample

answered Dec 5, 2020 at 14:37

2 votes

Accepted

Interpreting imputation result from GLIMPSE

answered Jan 1, 2022 at 11:33

2 votes

VCF file inspector app with GUI

answered Jan 6, 2022 at 20:32

2 votes

Accepted

Error: "fewer tokens than expected" while using --update-name flag in plink

answered Jun 10, 2021 at 12:49

2 votes

Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

answered Jul 17, 2021 at 11:35

2 votes

Accepted

Imputing 23andMe 3v data to v4 and v5?

answered Feb 15, 2022 at 10:47

Stack Exchange Network

49 Answers

How is the GT field in a VCF file defined?

What should be the numbers in the fastSTRUCTURE file?

How to convert a BAM file into a VCF file

what are the nodes and edges values in gene regulatory networks?

Extracting a column from a vcf file

Question about public availability of human SNP dataset with country of origin

Renaming samples in vcf file

Are variant calling files personally identifiable information?

Is there any database about the abundance of proteins in urine of healthy patients?

Tutorials on phasing and imputing low-coverage sequencing data

Download or create VCF from Human Genome Diversity Project (HGDP)

How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison

Imputing small region of the genome

BiocManager::install("DiffBind") mergeOne.c:341:3: note: use option -std=c99 or -std=gnu99 to compile your code

Problem with samtools command with a final hyphen

Reference for the statistical methodology used in joint genotype calling

correlation between imputed genotype and true genotype

Where can I download 30x 1000 genomes cram files?

Q: What analyses can I perform with a completely phased genome assembly?

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

Find overlap between VCF files

plink: --update-name vs. editing the BIM

Inheritance annotation for nsSNPs

How can I subset WGS data to the level of WES variants?

Summing up one column entries for each sample

Interpreting imputation result from GLIMPSE

VCF file inspector app with GUI

Error: "fewer tokens than expected" while using --update-name flag in plink

Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

Imputing 23andMe 3v data to v4 and v5?