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349 results • Page
1 of 7
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Filtering for tag:
variant
•
reset
0
votes
0
replies
31
views
mtDNA variant calling
variant
seq
mtdna
fasta
22 hours ago by
here_for_learning
• 0
5
votes
3
replies
213
views
How to force bcftools to call all variants
calling
bcftools
mpileup
variant
call
updated 7 days ago by
Istvan Albert
87k • written 7 days ago by
Hans
▴ 120
1
vote
3
replies
162
views
HaplotypeCallerSpark
Variant
gatk
haplotypecaller
updated 10 days ago by
Pierre Lindenbaum
135k • written 10 days ago by
quentin54520
• 0
2
votes
0
replies
154
views
Tool:
New location tracking tool for SARS-CoV-2 variant surveillance
tool
data
variant
covid-19
sars-cov-2
Tool
23 days ago by
ehaag
▴ 20
0
votes
3
replies
106
views
strange looking bcftools norm file
bcftools
bcftools norm
samtools
variant
5 weeks ago by
amy_houseman
▴ 20
1
vote
1
reply
126
views
Genomic Variant calling from RNA-Seq Data
RNA-Seq
SNP
Genomic
Variant
updated 6 weeks ago by
Kevin Blighe
72k • written 6 weeks ago by
hkarakurt
▴ 110
0
votes
3
replies
197
views
which tool should be used to call the genotype?
ngs
genotype
gatk
genotype calling
variant
updated 7 weeks ago by
Biostar
20 • written 3 months ago by
JENNIE
• 0
0
votes
2
replies
2.4k
views
[ti_index_core] the chromosome blocks not continuous at line xxxx, is the file sorted? [pos 1]
vcf
index
variant
updated 8 weeks ago by
Biostar
20 • written 3.1 years ago by
shubhra.bhattacharya
▴ 120
1
vote
1
reply
119
views
Filtering somatic variants (annotated VCF files)
VCF
somatic
filtering
variant
8 weeks ago by
g.zachwyc
• 0
1
vote
3
replies
1.2k
views
GATK SplitNCigarReads Error
gatk
RNA-Seq
variant
updated 9 weeks ago by
lucask3
▴ 20 • written 21 months ago by
BAGeno
▴ 180
0
votes
0
replies
195
views
Problems with overlapping variants in a vcf file
vcf
overlapping
bcftools
variant
10 weeks ago by
Buxus
▴ 10
0
votes
1
reply
94
views
Variant not annotated by ANNOVAR in the main transcript
Annovar
Variant
Annotation
Transcript
Exome
11 weeks ago by
geocarvalho
▴ 170
1
vote
2
replies
140
views
variant filtering based on high quality reference - removing false positives
sequence
genome
vcf
quality control
variant
12 weeks ago by
nobody
• 0
0
votes
1
reply
214
views
Creating in house database of variants
variant
clinical genomics
database
updated 3 months ago by
Pierre Lindenbaum
135k • written 3 months ago by
thisisinspiredme08
• 0
0
votes
1
reply
164
views
SnpSift set intersection with EFF annotations
snpsift
variant
annotation
parsing
3 months ago by
Richard
▴ 580
1
vote
7
replies
305
views
How to create vcf file with SNPs bed file and sorted bam file?
RNA-Seq
genome
variant
updated 4 months ago by
Qiongyi
▴ 110 • written 4 months ago by
O.rka
▴ 290
1
vote
1
reply
214
views
create an haplotype
snp
haplotype
variant
updated 4 months ago by
mansar_76
▴ 10 • written 12 months ago by
marmar
• 0
0
votes
0
replies
202
views
PacBio's variantCaller's vcf inconsistent with it's consensus sequence
pacbio
variant
variantCaller
vcf
consensus
updated 4 months ago by
Biostar
20 • written 5 months ago by
mark.rose
▴ 40
0
votes
1
reply
180
views
VEP repeated region flag
VEP
repeated-region
variant
human
updated 4 months ago by
Emily_Ensembl
22k • written 4 months ago by
cocchi.e89
▴ 140
8
votes
2
replies
689
views
What is the VEP Impact column?
VEP
sequencing
consequence
variant
ensembl
written 5 months ago by
nub6
▴ 20
3
votes
1
reply
210
views
Extract specific variant genome ID from a VCF file
variant
genome
vcf
updated 5 months ago by
Jorge Amigo
12k • written 5 months ago by
Chvatil
▴ 60
24
votes
0
replies
1.4k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
variant
interpretation
annotation
clinical
cancer
Tutorial
6 months ago by
Malachi Griffith
18k
2
votes
3
replies
308
views
Convert variant coordinates from one genome build to the other
sequence
variant
genome_build
6 months ago by
banerjeeshayantan
▴ 190
3
votes
7
replies
301
views
Where can I find Annotation info for VCF files?
alignment
gene
next-gen
sequencing
variant
7 months ago by
akshaykum684
▴ 20
3
votes
2
replies
638
views
VCF file analysis - Tutorial resources
variant
alignment
sequencing
sequence
next-gen
7 months ago by
akshaykum684
▴ 20
4
votes
4
replies
205
views
Different VCF file extensions - VCF 101
sequencing
snp
genome
gene
variant
7 months ago by
akshaykum684
▴ 20
1
vote
13
replies
367
views
How to allele frequency for each variant in VCF file
vcf
variant
genome
gene
perl
7 months ago by
Nyksubuz
▴ 10
0
votes
3
replies
264
views
How to calculate maf for a variant for case and control
MAF
genetics
variant
8 months ago by
MAPK
★ 1.7k
1
vote
4
replies
278
views
how to find snp changes between pairs of samples that have genomes sequenced
variant
genome
8 months ago by
bryanchang2016
▴ 20
0
votes
1
reply
262
views
difference between bcftools mpileup and bcftools call
bcftools
mpileup
call
variant
8 months ago by
sami
▴ 20
0
votes
0
replies
213
views
On the conventions for annotating the position of insertion and deletion variants
genotyping
indels
genomics
genome
variant
8 months ago by
kynnjo
▴ 40
0
votes
5
replies
213
views
Read showing Insertion of 41 bases when aligned with BWA
Variant
BWA
Bowtie2
updated 8 months ago by
swbarnes2
9.7k • written 8 months ago by
kspata
▴ 70
0
votes
2
replies
503
views
How to merge 2 VCF files that was previously extracted from same file
SNP
variant
software error
VCF
GATK
9 months ago by
phongphak.06
▴ 10
0
votes
0
replies
237
views
ANNOVAR issue annotating vcf
annover
variant
gnomad
9 months ago by
brismiller
▴ 40
1
vote
4
replies
325
views
bcftools filtering on INFO fields
variants
vcf
bcftools
variant
9 months ago by
Stephane Plaisance
▴ 440
0
votes
0
replies
190
views
Split phased haplotypes of same person coming from same parents
variant
haplotype
snp
indel
9 months ago by
Parham
★ 1.5k
1
vote
4
replies
212
views
Statistical meaning of top hit and top 10
gene
variant
score
10 months ago by
LimMo
▴ 10
0
votes
0
replies
273
views
Varscan2 somatic output annotation with snpEff -cancer option
sequencing
annotation
Variant
Varscan2
snpEff
10 months ago by
jobrien
• 0
1
vote
6
replies
487
views
STAR error (segmentation fault) in Aligning reads
NGS
STAR
READS
Variant
Alignment
11 months ago by
spriyansh29
▴ 30
1
vote
1
reply
391
views
determine exon number from variant genomic coordinates
exon
coordinates
variant
human
exome
updated 11 months ago by
rbagnall
★ 1.7k • written 11 months ago by
cocchi.e89
▴ 140
0
votes
5
replies
247
views
VEP MutationAssessor output
vep
MutationAssessor
variant
human
updated 12 months ago by
Ben_Ensembl
★ 1.6k • written 12 months ago by
cocchi.e89
▴ 140
0
votes
5
replies
2.9k
views
freebayes haplotype calling (phased variants)
freebayes
haplotype
phase
phased
variant
updated 12 months ago by
mikemc
▴ 10 • written 5.1 years ago by
mark.rose
▴ 40
8
votes
14
replies
3.8k
views
List Of Dbsnp Variants Where Reference Genome Has Minor Allele
reference
dbsnp
variant
exome
updated 12 months ago by
Biostar
20 • written 9.3 years ago by
Ana Rodrigues Grant
▴ 30
1
vote
1
reply
282
views
Extracting variant reads and reference reads quickly from mapped files
dna-seq
variant
12 months ago by
graeme.thorn
▴ 50
0
votes
3
replies
301
views
Pipes within VCF INFO Column
next-gen
VCF
Variant
SNP
Exome-Sequencing
updated 12 months ago by
GenoMax
99k • written 12 months ago by
basay3
• 0
8
votes
7
replies
3.8k
views
Why There Are A Lot Of Mq0 Reads In Some Particular Regions?
variant
calling
updated 12 months ago by
Biostar
20 • written 8.2 years ago by
lyz10302012
▴ 360
1
vote
3
replies
284
views
Sequence Conflict in Uniprot
Variant
Mutation
GWAS
Genomics
Sequencing
updated 13 months ago by
JC
12k • written 13 months ago by
Negin
▴ 10
0
votes
1
reply
291
views
callVariants problem with hg38 aligned bam: DEBUG - There are 0 filtered variant candidates in reads which overlap the region
Platypus
SNP
variant
13 months ago by
Paso
▴ 10
5
votes
3
replies
4.3k
views
Tool:
CRAVAT: a web tool to annotate and analyze cancer variants
sequencing
Cancer
annotation
variant
Tool
updated 13 months ago by
slcrick
▴ 240 • written 5.5 years ago by
Collin
▴ 890
0
votes
0
replies
313
views
Using SnpEff on Galaxy
NGS
Variant
VCF
assembly
SNP
14 months ago by
pmenon0998
• 0
349 results • Page
1 of 7
Recent Votes
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Answer: Tool to find chromosome specific repeats
Answer: What Is The Total Size Of Hgdownload.Cse.Ucsc.Edu/Gbdb/Mm9
Comment: correct way of analyzing cell proportions in singlecell data
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Recent Replies
Answer: Expression of gene of interest across conditions in single-cell data
by
jared.andrews07
9.1k
Take a look at [dittoSeq](http://www.bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html) for viz options - it…
Comment: Extracting only tumor samples from Single cell RNASeq
by
jared.andrews07
9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
Comment: Cell composition in each condition of single cell data
by
paria.alipour
▴ 20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering
by
GenoMax
99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br> https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data
by
rpolicastro
5.1k
The images seem to be missing from your post
Comment: Limma experiment design and making contrasts
by
kra277
• 0
Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts
by
Kevin Blighe
72k
Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts
by
kra277
• 0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation
by
brunobsouzaa
▴ 510
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic
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boczniak767
▴ 740
Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
Comment: should stop codon be counted as part of CDS
by
sullis02
• 0
Your github page appears to live here now https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
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by
Istvan Albert
87k
I am not all that knowledgeable of Cytoscapes features and scripting capabilities, but if it does not support that operation you can expo…
Comment: Creating reference genome for mapping and then selecting
by
Istvan Albert
87k
you would get the counts as you would get them in any other case, how do you know something maps to chromosome 1 of human genome? Because i…
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