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:
vcftools
•
reset
2
votes
5
replies
375
views
GATK - Output differences in Calls when Split by chromosome intervals and without splitting
GATK
PICARD
MergeVcf
vcftools
1 day ago by
Maverick
▴ 10
5
votes
15
replies
695
views
Merge VCF files by chromosome and Across samples
GATK
PICARD
MergeVcf
vcftools
14 days ago by
Maverick
▴ 10
0
votes
0
replies
279
views
VCFTools Order of Flags Inquiry
vcf
vcftools
updated 8 weeks ago by
Medhat
9.8k • written 8 weeks ago by
S
• 0
1
vote
10
replies
7.7k
views
6 follow
vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
vcftools
vcf
updated 12 weeks ago by
Ram
44k • written 6.1 years ago by
mayara.salvian
▴ 10
2
votes
4
replies
382
views
VCFtools warning message
vcftools
variant-calling
updated 3 months ago by
Ram
44k • written 3 months ago by
ashaneev07
▴ 40
6
votes
5
replies
8.2k
views
9 follow
How to convert .vcf files into .csv?
vcf
csv
sql
python
vcftools
updated 3 months ago by
zx8754
12k • written 7.5 years ago by
feng9oly
• 0
1
vote
1
reply
284
views
Discrepancies in F Coefficient and Heterozygosity Estimates
population-genetics
F-coefficient
plink
vcftools
updated 3 months ago by
Ram
44k • written 3 months ago by
eleftosi
• 0
0
votes
1
reply
265
views
Remove variants from vcf file does not work
bcftools
vcf
vcftools
updated 4 months ago by
Ram
44k • written 4 months ago by
8armed
▴ 20
2
votes
3
replies
456
views
VCFtools indels/SNP treatment
variants
vcftools
updated 4 months ago by
Jeremy Leipzig
22k • written 4 months ago by
draccident
• 0
1
vote
4
replies
446
views
Subset VCF to exon region but still get intron_variant annotation
Ensembl
vcf
VEP
vcftools
updated 4 months ago by
rfran010
★ 1.3k • written 4 months ago by
tomas4482
▴ 430
5
votes
3
replies
5.3k
views
bcftools to remove non-variants sites
bcftools
SNP
vcftools
vcf
filter
updated 4 months ago by
zx8754
12k • written 4.1 years ago by
shiy05
▴ 30
0
votes
0
replies
299
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
6 months ago by
rijan_dhakal2055
▴ 10
1
vote
3
replies
3.0k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller
GATK
Plink1.9
vcftools
updated 7 months ago by
Jingjingzhang
• 0 • written 2.7 years ago by
ramshahaya
▴ 10
0
votes
2
replies
920
views
Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 a…
vcftools
updated 7 months ago by
Pierre Lindenbaum
164k • written 7 months ago by
juan.sainz
• 0
1
vote
1
reply
538
views
Filtering VCF files with bcftools
VCF
vcftools
bcftools
updated 7 months ago by
4galaxy77
2.8k • written 7 months ago by
eleni.psar
• 0
0
votes
5
replies
720
views
Issues filtering VCF file with bcftools/vcftools
vcftools
vcf
bcftools
updated 7 months ago by
Pierre Lindenbaum
164k • written 7 months ago by
ekirsch
• 0
5
votes
5
replies
1.5k
views
long view SNPs in vcf file
bcftools
Variant-Calling
SNP
freebayes
vcftools
updated 8 months ago by
yzliu01
▴ 10 • written 24 months ago by
young_bioinformatician
▴ 240
0
votes
4
replies
758
views
how to extract variants from the vcf.gz files linked below?
vcftools
bcf
vcf
bcftools
8 months ago by
Mahad
• 0
0
votes
6
replies
793
views
vcftools warnings worrisome?
vcftools
updated 8 months ago by
Ram
44k • written 8 months ago by
8armed
▴ 20
2
votes
7
replies
760
views
Extract SNPs present in mutants
snp
vcftools
vcf
bcftools
updated 8 months ago by
Pierre Lindenbaum
164k • written 8 months ago by
pablo
▴ 310
1
vote
2
replies
520
views
vcf-validator could not parse the alleles
vcf-validator
vcftools
vcf
8 months ago by
ekirsch
• 0
1
vote
4
replies
1.3k
views
Different relatedness estimates by PLINK and VCFTOOLS despite same method
kinship
vcftools
PLINK
relatedness
8 months ago by
8armed
▴ 20
1
vote
2
replies
396
views
How can I view the information in an alternative allele?
vcftools
bcftools
VCF
annovar
updated 9 months ago by
Ram
44k • written 9 months ago by
iarmir
▴ 10
0
votes
2
replies
4.9k
views
VCFtools calculate SNP density
vcf
snp
vcftools
snp-density
updated 9 months ago by
ahusnoo
• 0 • written 5.9 years ago by
christinachavez
• 0
4
votes
8
replies
1.1k
views
Isolating and extracting regions in VCF file
ANNOVAR
vcftools
bcftools
GATK
VCF
updated 9 months ago by
Jeremy Leipzig
22k • written 9 months ago by
iarmir
▴ 10
0
votes
0
replies
319
views
How to use --chr flag (vcftools --LROH) with a vcf file that uses scaffold notation
vcftools
scaffold
ROH
9 months ago by
ekirsch
• 0
0
votes
7
replies
1.0k
views
Search for specific SNPs in VCF files of patients.
ANNOVAR
vcftools
bcftools
GATK
VCF
updated 10 months ago by
Ram
44k • written 10 months ago by
iarmir
▴ 10
0
votes
0
replies
373
views
Error: Require Genotypes in VCF file in order to output IMPUTE format.
vcftools
VCF
updated 10 months ago by
Ram
44k • written 10 months ago by
Warrenkb
• 0
0
votes
1
reply
587
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
updated 10 months ago by
Ram
44k • written 11 months ago by
S
▴ 10
1
vote
5
replies
764
views
vcftools
vcftools
updated 11 months ago by
Barista
▴ 10 • written 11 months ago by
sevda
• 0
1
vote
7
replies
1.1k
views
help with weird PCA? (vcfR)
vcftools
vcfR
R
11 months ago by
MaeBH
• 0
0
votes
5
replies
1.0k
views
how to assign chromosome-level annotation to a genome organised by contig?
vcftools
updated 12 months ago by
dthorbur
★ 2.5k • written 12 months ago by
violeta.caballero.lopez
• 0
1
vote
2
replies
654
views
Restricting vcf entries based on ID length
bcftools
vcf
vcftools
updated 13 months ago by
chrchang523
11k • written 14 months ago by
ethan.kreuzer
• 0
0
votes
2
replies
571
views
Extract reference and alternate SNPs for different samples
vcftools
bcftools
SNPs
updated 14 months ago by
GenoMax
146k • written 14 months ago by
gubrins
▴ 350
32
votes
7
replies
22k
views
6 follow
VCF merge or concatenate?
snp
VCF
VCFTools
written 5.3 years ago by
rokragna295
▴ 80
0
votes
1
reply
701
views
Plotting relatedness2 output in R
vcftools
relatedness2
nodes
R
updated 15 months ago by
GenoMax
146k • written 15 months ago by
Whirlingdaf
▴ 60
0
votes
1
reply
604
views
VCFTools MAF Filter needs Efficiency Inquiry
vcf
maf
vcftools
updated 15 months ago by
chrchang523
11k • written 15 months ago by
S
• 0
0
votes
3
replies
1.3k
views
Efficient Way to Split Huge VCF Files by Chromosome | Inquiry
htslib
bcftools
vcftools
vcf
tabix
15 months ago by
S
• 0
0
votes
2
replies
552
views
Too high number of SNPs using ddRAD data (36 cattle)
ddrad
samtools
snp
vcftools
15 months ago by
ymberzal
• 0
0
votes
2
replies
757
views
vcftools - Fst statistics
vcftools
updated 15 months ago by
Ram
44k • written 15 months ago by
Lukas
▴ 130
2
votes
4
replies
728
views
Filter VCF file for variant alleles
VCF
bcftools
vcftools
updated 16 months ago by
Ram
44k • written 17 months ago by
miguellarrazlopezdenovales
▴ 20
1
vote
2
replies
2.6k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 17 months ago by
barslmn
★ 2.3k • written 7.0 years ago by
shrutishreyajha
▴ 10
2
votes
5
replies
1.2k
views
vcftools on 2 snpeff vcf files
snpeff
vcftools
updated 16 months ago by
Ram
44k • written 18 months ago by
anasjamshed
▴ 140
0
votes
0
replies
419
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftools
updated 16 months ago by
Ram
44k • written 19 months ago by
Nai
▴ 50
0
votes
0
replies
709
views
Admixture error in removing loci with no genotypes even after filtering loci
plink
ADMIXTURE
vcftools
updated 16 months ago by
Ram
44k • written 20 months ago by
Whirlingdaf
▴ 60
22
votes
8
replies
42k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 14 months ago by
Bioinformatics_NewComer
▴ 330 • written 12.2 years ago by
bioinfo
▴ 840
0
votes
4
replies
1.8k
views
From VCF to BEAGLE format with multiple chromosomes
vcf
vcftools
beagle
gvcf
17 months ago by
Begonia_pavonina
▴ 200
0
votes
2
replies
679
views
Filetering low reads from vcf file/ download exonic region, coding regions of GRCh38 - hg38
picard
gatk
vcftools
mutect2
21 months ago by
minoo
▴ 10
0
votes
0
replies
1.0k
views
Extract different variants of a vcf file comparing to other vcf files
bedtools
mutect2
vcftools
gatk
updated 16 months ago by
Ram
44k • written 21 months ago by
minoo
▴ 10
0
votes
3
replies
760
views
Reomve the first occurance of overalapping variants from VCF file
vcf
vcftools
updated 21 months ago by
mohammadhassanj
▴ 260 • written 21 months ago by
Frieda
▴ 60
50 results • Page
1 of 1
Recent Votes
Comment: Finding Differential Phosphosites in TMT Phosphoproteomics Data
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
A: How do I ask a question on Biostars?
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Answer: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
Recent Locations •
All
Macao,
6 minutes ago
Netherlands,
6 minutes ago
United Kingdom,
10 minutes ago
Hong Kong,
16 minutes ago
India,
22 minutes ago
United Kingdom,
35 minutes ago
Norway,
35 minutes ago
Recent Awards •
All
Popular Question
to
wangziwei0010
▴ 30
Popular Question
to
xiaoleiusc
▴ 140
Popular Question
to
odi
▴ 10
Popular Question
to
Alewa
▴ 170
Popular Question
to
Ezequiel
▴ 10
Popular Question
to
pablo
▴ 310
Popular Question
to
Jichen Wen
▴ 30
Recent Replies
Comment: Magnesium ion in a post-docking adjustment
by
dthorbur
★ 2.5k
[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
• 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
Comment: How to determine whether it is 10x data
by
king
• 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
Chen
• 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
GenoMax
146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
Comment: Statistical test to be used for dataset
by
allingt
• 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
Comment: dittoHeatmap; adding column labels on the heatmap
by
jared.andrews07
★ 18k
I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type
by
allingt
• 0
What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
Comment: Genes of Interest in a Multi-Tissue Analysis
by
allingt
• 0
The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
Comment: WGCNA: Why are my brown, yellow, and other modules not visible in the gene dendr
by
allingt
• 0
Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
Comment: Why does WGCNA use weighted correlation instead of Pearson correlation?
by
allingt
• 0
The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
Comment: dittoHeatmap; adding column labels on the heatmap
by
Varun Gupta
★ 1.3k
any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
Comment: How can I determine the p-value of genes within each identified module in WGCNA?
by
allingt
• 0
What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is
by
i.sudbery
20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
Traffic: 1506 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