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109 results • Page
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Showing :
WES
•
reset
0
Votes
1
Reply
387
Views
TCGA TMB: What exome size to use?
WES
2.0 years ago
ngs_engineer
• 0
• updated 20 months ago
bastien.nguyen
• 0
3
Votes
13
Replies
263
Views
VarScan warning and exit after Invalid format for pileup at line 1
WES
software error
variant calling
22 months ago
n.tear
• 0
• updated 21 months ago
Biostar
20
0
Votes
2
Replies
1.1k
Views
converting varscan2 output to sequenza
exome
WES
mutation
SNP
3.5 years ago
a01039012387
• 10
• updated 21 months ago
brunobsouzaa
• 10
2
Votes
3
Replies
183
Views
EXCAVATOR shows 1 deletion which is not TRUE in IGV
excavator
igv
wes
exome
cnv
21 months ago
lait
• 130
2
Votes
4
Replies
190
Views
bionano hybrid scaffold
WES
bionano
optical mapping
illumina
22 months ago
lait
• 130
• updated 22 months ago
WouterDeCoster
39k
2
Votes
1
Reply
205
Views
Mutect2 "somatic" variants with resistant tissue culture lines
mutect2
wes
variants
genotyping
GATK
23 months ago
shawn.w.foley
• 670
• updated 22 months ago
Biostar
20
2
Votes
2
Replies
316
Views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
22 months ago
stephaniem
• 0
0
Votes
0
Replies
107
Views
Tools to access variation of ploidy at certain genomic loci using WES
WES
Ploidy
Endomitosis
22 months ago
Rahul Sharma
• 580
0
Votes
2
Replies
165
Views
Can CVNkit call CNV correctly at HLA genes region?
CNVKIT
wes
HLA
22 months ago
MatthewP
• 110
• updated 22 months ago
linouhao
• 0
3
Votes
2
Replies
175
Views
Post-filtering WES for mutation calling
mutect2
wxs
wes
22 months ago
graeme.thorn
• 40
0
Votes
0
Replies
167
Views
How can I check my title of reads added by BWA mem -R?
WES
BWA
22 months ago
Laven9
• 0
3
Votes
4
Replies
571
Views
Downstream analysis of VCF files obtained from VarScan2
WES
VCF
Somatic variations
VarScan2
SnpEff
2.3 years ago
Raheleh
• 70
• updated 23 months ago
bari.ballew
• 90
8
Votes
4
Replies
298
Views
tool to detect large deletions
deletions
IGV
wes
23 months ago
lait
• 130
• updated 23 months ago
bari.ballew
• 90
0
Votes
1
Reply
1.3k
Views
Annovar - Mouse Exome Sequencing
annovar
wes
whole-exome sequencing
mouse
3.7 years ago
cbatist
• 0
• updated 23 months ago
Kevin Blighe
43k
6
Votes
1
Reply
1.6k
Views
Gold Standard for Human cancer exome sequencing
WES
Somatic
MuTect
VarScan
Cancer
4.3 years ago
Jerome Lin
• 20
• updated 23 months ago
Biostar
20
7
Votes
4
Replies
202
Views
Can you use germline variation calling on a normal embryonic stem cell line?
SNP
WES
embryonic cell
germline variation
GATK
23 months ago
maria2019
• 30
• updated 23 months ago
Emily_Ensembl
18k
0
Votes
6
Replies
226
Views
why does qualimap2 shows different results for number of mismatches for bowtie2 and BWAMEM?
WES
qualimap
bowtie2
bwamem
23 months ago
maria2019
• 30
• updated 23 months ago
h.mon
25k
0
Votes
1
Reply
163
Views
Should I use the same reference indexing command of bwa for WGS and WES analysis?
bwa mem
indexing
WGS
WES
23 months ago
maria2019
• 30
• updated 23 months ago
finswimmer
11k
0
Votes
1
Reply
177
Views
How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
SNP
hESC
WES
samtools
23 months ago
maria2019
• 30
1
Vote
4
Replies
578
Views
What is the right illumina universal adapter sequence for trimming paired-end reads?
WES
fastqc
trimadaptor
23 months ago
maria2019
• 30
• updated 23 months ago
Vijay Lakhujani
4.1k
3
Votes
2
Replies
203
Views
Does strange fastQC GC content report cause a problem for WES analysis?
fastQC
WES
GC content
23 months ago
maria2019
• 30
• updated 23 months ago
JC
7.9k
2
Votes
5
Replies
201
Views
Should I specify exome region to do the QC with qualimap2 for WES analysis?
qualimap2
WES
QC
23 months ago
maria2019
• 30
• updated 23 months ago
h.mon
25k
3
Votes
10
Replies
371
Views
How can I split WES FASTQ file into sub-files for each chromosome ?
WES
split
fastq
chromosome
23 months ago
Laven9
• 0
1
Vote
0
Replies
191
Views
putative mosaic mutations
mosaic
de novo
wes
sequencing
2.0 years ago
lait
• 130
1
Vote
2
Replies
236
Views
Incorrect number of AD fields (2) at 1:878906 cannot merge
bcftools
vcf
WES
2.0 years ago
jaybee
• 10
1
Vote
1
Reply
1.3k
Views
What are the best tools/practices for CNV (structural variation) detection/analysis for Illumina family data?
cnv
sv
snp array
wes
wgs
3.7 years ago
Irina Astrovskaya
• 20
• updated 2.2 years ago
h.mon
25k
4
Votes
6
Replies
721
Views
Appropriate bed files from library capture kit for computing on target coverage of WES bam files with Picard and CollectHsMetrics
Picard
WES
bam files
on target coverage
NGS
2.2 years ago
svlachavas
• 560
• updated 2.2 years ago
finswimmer
11k
1
Vote
6
Replies
928
Views
Converting TCGA Bam files to fastq: Picard does not work!
wes
sequencing
3.6 years ago
jonessara770
• 150
• updated 2.3 years ago
rmh1995
• 0
0
Votes
0
Replies
320
Views
Qs about mutect2
WES
mutect2
gatk
2.4 years ago
walker
• 20
0
Votes
3
Replies
276
Views
Enrichment platforms for 1000GP exome data
data
WES
2.4 years ago
kuckunniwid
• 40
3
Votes
6
Replies
773
Views
CNV calling from exome sequencing data with a low number of samples
WES
CNV
exome
copy-number variant
2.4 years ago
KumaraFM
• 0
• updated 2.4 years ago
toralmanvar
• 760
1
Vote
3
Replies
1.6k
Views
SciClone on WES data
sciclone
wes
clonality
varscan
dnacopy
3.8 years ago
mar.ark.parr
• 30
• updated 2.4 years ago
aliz0611
• 0
15
Votes
8
Replies
1.8k
Views
Whole exome sequencing data, rare variants and QQ-plots
QQ-plot
whole exome sequencing
WES
4.7 years ago
felejohs
• 70
• updated 2.4 years ago
zx8754
7.5k
1
Vote
1
Reply
375
Views
my bam file contains both single-end and paired-end. How can I convert bam to fastq so that fastq contains only paired-end reads?
WES
2.5 years ago
jonessara770
• 150
• updated 2.5 years ago
Pierre Lindenbaum
120k
0
Votes
3
Replies
401
Views
differences in covered regions in exome and whole genome sequencing
exome-sequencing
WES
genome-sequencing
WGS
2.6 years ago
miaowzai
• 130
• updated 2.5 years ago
Biostar
20
0
Votes
1
Reply
417
Views
Database of Mutations and the associated drugs
WES
ngs
2.5 years ago
Ron
• 950
• updated 2.5 years ago
Kevin Blighe
43k
0
Votes
1
Reply
404
Views
CNV analysis from exome sequencing data
cnv
wes
2.6 years ago
mkamranazim
• 0
1
Vote
1
Reply
319
Views
Haplotype sharing of mutation carriers
ngs
haplotype
SNP
WES
2.6 years ago
Lio04
• 0
• updated 2.6 years ago
Kevin Blighe
43k
1
Vote
3
Replies
374
Views
interpretation of intronic variant detected by WES
WES
2.6 years ago
jonessara770
• 150
0
Votes
1
Reply
259
Views
How to remove Variants where the Ref and Alt in the reference genome are switched?
NGS
WES
VariantCalling
RefAlt
2.6 years ago
O.ibra
• 0
• updated 2.6 years ago
Pierre Lindenbaum
120k
2
Votes
5
Replies
1.0k
Views
Implementation of the COSMIC database for somatic variant annotation and filtering pipeline for WES cancer data
somatic variants
COSMIC
variant annotation
WES
2.7 years ago
svlachavas
• 560
2
Votes
2
Replies
594
Views
How to take in consideration UMI in WES pipeline?
WES
2.8 years ago
jonessara770
• 150
• updated 2.8 years ago
i.sudbery
4.7k
0
Votes
0
Replies
451
Views
Read simulators for Ion Torrent platform specific for WES
simulation
WES
Ion
Torrent
AmliSeq
2.8 years ago
world_genesis
• 0
6
Votes
2
Replies
655
Views
IBD calculation indicates cryptic relatedness of 1 Individual with all others within a sequencing cohort
WES
IBD
Plink
Relatedness
2.8 years ago
maegsul
• 140
• updated 2.8 years ago
chrchang523
5.2k
4
Votes
4
Replies
681
Views
sample mixing when demultiplexing
demultiplex
WES
human samples
NGS
BAM
3.0 years ago
lait
• 130
0
Votes
4
Replies
506
Views
low coverage & BAF plots have three peaks
b-allele frequency
low coverage
WES
human samples
3.0 years ago
lait
• 130
0
Votes
1
Reply
461
Views
CNVkit segmetrics error
CNV
WES
germline
3.0 years ago
SPDouglas
• 0
• updated 3.0 years ago
Eric T.
♦ 2.4k
0
Votes
8
Replies
616
Views
Create a custom exome .genome for IGV
IGV
exome
sequencing
WES
3.0 years ago
jgarces
• 10
• updated 3.0 years ago
h.mon
25k
1
Vote
2
Replies
1.2k
Views
I need allele copy number information for running PyClone
copy number
allele
WES
whole-exome
3.6 years ago
a01039012387
• 10
• updated 3.0 years ago
nilesh.gardi2688
• 0
0
Votes
0
Replies
346
Views
High CG>CA and CG>TG errors from bait bias WES
WES
bias
3.0 years ago
maduh17
• 10
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