Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
50 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
Showing top results for tag:
SNPS
•
reset
1
vote
8
replies
339
views
Beagle Gives Error no matter what i do
Beagle
Impute
SNPs
5 days ago by
Emilie
▴ 10
0
votes
7
replies
353
views
Snippy does not find SNPs I know are present
snippy-multi
snippy
snps
updated 5 days ago by
Michael
55k • written 5 days ago by
blur
▴ 280
0
votes
2
replies
255
views
SNPs profile on chromosome 1 curve
profile
SNPs
updated 11 days ago by
Brian Bushnell
20k • written 18 days ago by
Nuglozeh
▴ 10
0
votes
1
reply
361
views
Less stringent way of calling variants in PacBio data
bcftools
SNPs
variant
PacBio
10X
updated 26 days ago by
dthorbur
★ 2.4k • written 4 weeks ago by
TheCatalyst
• 0
5
votes
3
replies
237
views
Assistance with Identifying Human Orthologs of Catle SNPs
Orthologs
SNPs
Catle
Human
updated 26 days ago by
GenoMax
145k • written 26 days ago by
Star:)
▴ 50
0
votes
0
replies
208
views
Classify SNPs from PacBio data
SNPs
PacBio
GEX
pigeon
10X
4 weeks ago by
TheCatalyst
• 0
0
votes
2
replies
253
views
Seeking Opinions on Pipeline for Detecting Somatic Variants and Rare Germline Mutations
snps
germline
somatic
gatk
7 weeks ago by
George
▴ 10
0
votes
0
replies
154
views
Heterozygous SNPs Allele Balance Threshold
SNPs
Genomics
WES
Allele
updated 9 weeks ago by
Ram
44k • written 9 weeks ago by
menyawino
• 0
0
votes
0
replies
201
views
News:
Online course: Conservation Genomics
SNPs
PopulationGenomics
ConservationGenomics
inbreeding
3 months ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
179
views
News:
Conservation Genomics course
SNPs
PopulationGenomics
ConservationGenomics
inbreeding
4 months ago by
carlopecoraro2
★ 2.6k
0
votes
1
reply
264
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 4 months ago by
zx8754
12k • written 4 months ago by
Ali
• 0
2
votes
0
replies
246
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
4 months ago by
carlopecoraro2
★ 2.6k
0
votes
2
replies
386
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
5 months ago by
dtnondorf
• 0
1
vote
5
replies
629
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
5 months ago by
Riccardo
▴ 10
4
votes
11
replies
1.3k
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
4 months ago by
J
▴ 10
3
votes
3
replies
733
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 months ago by
swbarnes2
14k • written 5 months ago by
noodle
▴ 590
1
vote
1
reply
440
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 5 months ago by
LChart
4.3k • written 5 months ago by
George
▴ 10
2
votes
6
replies
769
views
Need help understanding core SNPs
SNPs
snippy
6 months ago by
ujichu
• 0
0
votes
1
reply
328
views
How to get population specific SNPs from a vcf file
specific
SNPs
population
updated 7 months ago by
Pierre Lindenbaum
164k • written 7 months ago by
291796256
• 0
1
vote
1
reply
421
views
filter 1000 genome vcf file to keep common snps
bcftools
SNPs
updated 8 months ago by
Ram
44k • written 8 months ago by
shersky
• 0
1
vote
1
reply
462
views
Extract cis and trans mutations from bam file
Mutations
BAM
VCF
SNPS
updated 9 months ago by
GenoMax
145k • written 9 months ago by
RD
▴ 20
27
votes
8
replies
1.7k
views
6 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics
snps
survey
papers
updated 3 months ago by
Rob
6.9k • written 9 months ago by
Raony Guimarães
★ 1.4k
3
votes
4
replies
804
views
Where can I get a list of SNPs mapping overlapping genes in humans?
SNPs
updated 9 months ago by
Alex Reynolds
35k • written 9 months ago by
Mr Locuace
▴ 180
2
votes
4
replies
814
views
Alternatives to snpflip to find ambigious and flipped snps
gwas
plink
snps
snpflip
updated 10 months ago by
GenoMax
145k • written 10 months ago by
d.s.zimmerman
• 0
1
vote
6
replies
1.2k
views
A question about genotyping rate
genotyping
snps
harmonizer
array
11 months ago by
abedkurdi10
▴ 190
1
vote
2
replies
700
views
How do I remove duplicate SNPs in PLINK from more than 1 data set?
SNPs
Plink
11 months ago by
u19010843
• 0
1
vote
3
replies
1.3k
views
Computing Tajima's D from haploid SNPs
Haploid
SNPs
updated 11 months ago by
Prash
▴ 280 • written 3.3 years ago by
drowl1
▴ 30
3
votes
2
replies
642
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 12 months ago by
luffy
▴ 130 • written 12 months ago by
_quantum_girl_
▴ 40
1
vote
1
reply
515
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 12 months ago by
dthorbur
★ 2.4k • written 12 months ago by
am29
▴ 40
0
votes
0
replies
370
views
simuations with sim1000g
snps
simulation
sim1000G
chromosome
12 months ago by
Eliza
▴ 30
0
votes
2
replies
560
views
Extract reference and alternate SNPs for different samples
vcftools
bcftools
SNPs
updated 12 months ago by
GenoMax
145k • written 12 months ago by
gubrins
▴ 340
3
votes
3
replies
856
views
How to find variants in a specific gene in a cohort of 500k+ individuals?
variants
plink
SNPs
CNV
updated 13 months ago by
Pierre Lindenbaum
164k • written 13 months ago by
_quantum_girl_
▴ 40
3
votes
4
replies
878
views
simulation of chromosome
snps
simulation
chromosome
13 months ago by
Eliza
▴ 30
1
vote
2
replies
1.3k
views
QC Illumina EPIC array: Removing SNPs at CpG sites
SNPs
methylation
QC
Illumina
EPIC
updated 14 months ago by
Zhenyu Zhang
★ 1.2k • written 14 months ago by
kaaz
• 0
2
votes
2
replies
563
views
W,M,R nucleotides
variants
SNPs
genetics
updated 14 months ago by
GenoMax
145k • written 14 months ago by
harry.smith
• 0
0
votes
0
replies
311
views
Transform txt files with SNPs from ForenSeq kit to proper format for plink
plink
python
SNPs
15 months ago by
dzisis1986
▴ 70
0
votes
5
replies
1.3k
views
Error message when running a GATK SelectVariants: no positional argument is defined for this tool
GATK
SNPs
updated 15 months ago by
Ram
44k • written 15 months ago by
mohsamir2016
▴ 30
1
vote
5
replies
1.1k
views
rank SNPs after elastic net modeling
SNPs
R
elastic-net
modeling
updated 15 months ago by
Shred
★ 1.5k • written 15 months ago by
rheab1230
▴ 140
0
votes
2
replies
868
views
Extract samples from a VCF file that contain marker
bcftools
SNPs
updated 15 months ago by
WouterDeCoster
47k • written 15 months ago by
Cèlia
• 0
0
votes
0
replies
398
views
Correction for among sample/chromosomes for sequenicng depth, when comparing between samples or animals
GATK
SNPs
15 months ago by
mohsamir2016
▴ 30
0
votes
1
reply
529
views
ABO alleles
ABO
variants
SNPs
alleles
updated 16 months ago by
Raony Guimarães
★ 1.4k • written 16 months ago by
Fernando
• 0
0
votes
2
replies
727
views
Variant calling in WES vs WGS
snpEff
WGS
SNPs
WES
updated 16 months ago by
Prash
▴ 280 • written 16 months ago by
fifty_fifty
▴ 70
1
vote
2
replies
896
views
Read depth extraction
SNPs
Genomics
updated 16 months ago by
Ram
44k • written 16 months ago by
vlip
• 0
1
vote
4
replies
820
views
My VCF file structure is strange and less compatible to data processing programs.
VCF
GATK
SNPs
updated 16 months ago by
Istvan Albert
101k • written 16 months ago by
kgwkk2
• 0
0
votes
0
replies
444
views
Plink1.9, keeping order of updated samples IDs
SNPs
samples
Plink
17 months ago by
AMARU
• 0
0
votes
0
replies
405
views
Extracting common genotype testing SNPs from whole exome or genome data
testing
genotype
genome
exome
snps
17 months ago by
Moe
▴ 10
1
vote
2
replies
1.0k
views
kinship coefficient negative in multi-sample VCF from exome sequencing
SNPs
KING
sequencing
relatedness
exome
17 months ago by
AMARU
• 0
0
votes
0
replies
344
views
Identifying tagging variants / haplotypes in GWAS data
SNPs
GWAS
LD
haplotypes
plink
19 months ago by
Christopher
• 0
1
vote
8
replies
1.5k
views
Merge vcfs and retain only specific regions
SNPs
vcf
updated 19 months ago by
Ram
44k • written 19 months ago by
Whirlingdaf
▴ 60
0
votes
2
replies
616
views
Perform Plink association tests on a genetype file with one allele
plink
genetic-association-test
snps
19 months ago by
davidenoma
▴ 50
50 results • Page
1 of 1
Recent Votes
C: Single rare variant approaches
C: Single rare variant approaches
Answer: Importing data from GEO
Importing data from GEO
A: 0 Features for COVID-19 ExpressionSet through GEOQuery
0 Features for COVID-19 ExpressionSet through GEOQuery
Comment: trying to use the API for edirect tool (NCBI)
Recent Locations •
All
United States,
just now
UCLA,
6 minutes ago
Sydney, Australia.,
9 minutes ago
United States,
10 minutes ago
Australia,
10 minutes ago
United States,
23 minutes ago
United States,
24 minutes ago
Recent Awards •
All
Popular Question
to
sci
• 0
Popular Question
to
mykle hoban
▴ 40
Popular Question
to
avelarbio46
▴ 30
Popular Question
to
gcooper1245
▴ 10
Popular Question
to
ipediez93
▴ 40
Popular Question
to
David Langenberger
11k
Popular Question
to
mrashad
▴ 80
Recent Replies
Answer: featureCounts segmentation fault
by
Mensur Dlakic
★ 28k
It is very difficult to follow al the lines as your script content are not properly formatted. It appears that in one command you are do…
Comment: Using GEOquery
by
ATpoint
84k
Have you even read my answer? I gave a full explanation on what the problem is and what the solutions can be. What is unclear?
Comment: Using GEOquery
by
Rohulla
• 0
I also come up with this problem. No body still answer this question.
Answer: Performing Needleman-Wunsch Global Alignment for multiple mutant proteins agains
by
Istvan Albert
101k
You can use the `bio` with the `align` tool. Install with `pip install bio` then bio align query.fa target.fa You can put all the tar…
Answer: Long-read sequencing data simulation using CAMISIM
by
Istvan Albert
101k
Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
Comment: RNA-Seq mutation calling without germline data
by
marionette.kent
• 0
Thanks @shred for sharing your pipeline. Can I ask if it runs each sample individually? Our HPC has limited space for each user so I have b…
Comment: Pedigree information
by
bk11
★ 3.0k
Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the `.fam` file. If that information is missing an…
Comment: The Evolution of NGS: What’s New and What’s Next?
by
i.sudbery
20k
I know its a technical possiblity. But people I know that do this say its still very much an experimental technique. You need to learn the …
Answer: Merging bfiles
by
bk11
★ 3.0k
If you have common set of SNPs between your two set of bfiles `(PLINK files)`, you can use `plink --bmerge` command to merge them as follow…
Comment: The Evolution of NGS: What’s New and What’s Next?
by
Istvan Albert
101k
`rust` was not designed to be a competitor to `python`, it was designed as a competitor to `C` and `C++` - `rust` integrates really well…
Comment: Can someone install me (remotely) Amber24?
by
Ram
44k
Do you mean you have a Windows machine that has Windows Subsystem for Linux and you're unable to install a piece of software over a remote …
Comment: Choosing the Best Method for DEG Analysis: limma vs. DESeq2 for RSEM Normalized
by
Istvan Albert
101k
Fundamentally these types of filterings come down to the effect they have on the data. Does your filtering change the data, does it chang…
Comment: Generally how are non-canonical chromosomes treated in human variation studies
by
GenoMax
145k
This blog post may partly help: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Do you think that I should be including the information from the scaffold patch for the quantification? Initially I used the transcript_to_…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
by
GenoMax
145k
It has been moved to a comment (looks like you are a moderator that seems to have come back after a long break). You can accept @dgtool ans…
Traffic: 1234 users visited in the last hour
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