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Showing : WES • reset
0
Votes
1
Reply
384
Views
TCGA TMB: What exome size to use?
WES
20 months ago
ngs_engineer • 0 • updated 16 months ago
bastien.nguyen • 0
3
Votes
13
Replies
256
Views
VarScan warning and exit after Invalid format for pileup at line 1
WES software error variant calling
18 months ago
n.tear • 0 • updated 17 months ago
Biostar 20
0
Votes
2
Replies
1.1k
Views
converting varscan2 output to sequenza
exome WES mutation SNP
3.2 years ago
a01039012387 • 10 • updated 17 months ago
brunobsouzaa • 10
2
Votes
3
Replies
182
Views
EXCAVATOR shows 1 deletion which is not TRUE in IGV
excavator igv wes exome cnv
17 months ago
lait • 130
2
Votes
4
Replies
189
Views
bionano hybrid scaffold
WES bionano optical mapping illumina
18 months ago
lait • 130 • updated 18 months ago
WouterDeCoster 39k
2
Votes
1
Reply
204
Views
Mutect2 "somatic" variants with resistant tissue culture lines
mutect2 wes variants genotyping GATK
18 months ago
shawn.w.foley • 670 • updated 18 months ago
Biostar 20
2
Votes
2
Replies
316
Views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
18 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
18 months ago
Rahul Sharma • 580
0
Votes
2
Replies
165
Views
Can CVNkit call CNV correctly at HLA genes region?
CNVKIT wes HLA
18 months ago
MatthewP • 110 • updated 18 months ago
linouhao • 0
3
Votes
2
Replies
172
Views
Post-filtering WES for mutation calling
mutect2 wxs wes
18 months ago
graeme.thorn • 40
0
Votes
0
Replies
166
Views
How can I check my title of reads added by BWA mem -R?
WES BWA
18 months ago
Laven9 • 0
3
Votes
4
Replies
567
Views
Downstream analysis of VCF files obtained from VarScan2
WES VCF Somatic variations VarScan2 SnpEff
23 months ago
Raheleh • 70 • updated 18 months ago
bari.ballew • 90
8
Votes
4
Replies
298
Views
tool to detect large deletions
deletions IGV wes
18 months ago
lait • 130 • updated 18 months ago
bari.ballew • 90
0
Votes
1
Reply
1.3k
Views
Annovar - Mouse Exome Sequencing
annovar wes whole-exome sequencing mouse
3.4 years ago
cbatist • 0 • updated 19 months ago
Kevin Blighe 43k
6
Votes
1
Reply
1.6k
Views
Gold Standard for Human cancer exome sequencing
WES Somatic MuTect VarScan Cancer
4.0 years ago
Jerome Lin • 20 • updated 19 months ago
Biostar 20
7
Votes
4
Replies
200
Views
Can you use germline variation calling on a normal embryonic stem cell line?
SNP WES embryonic cell germline variation GATK
19 months ago
maria2019 • 30 • updated 19 months ago
Emily_Ensembl 18k
0
Votes
6
Replies
224
Views
why does qualimap2 shows different results for number of mismatches for bowtie2 and BWAMEM?
WES qualimap bowtie2 bwamem
19 months ago
maria2019 • 30 • updated 19 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
19 months ago
maria2019 • 30 • updated 19 months ago
finswimmer 11k
0
Votes
1
Reply
174
Views
How many SNPs I should expect to see in a normal human embryonic stem cell (hESC) with WES analysis?
SNP hESC WES samtools
19 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
19 months ago
maria2019 • 30 • updated 19 months ago
Vijay Lakhujani 4.1k
3
Votes
2
Replies
199
Views
Does strange fastQC GC content report cause a problem for WES analysis?
fastQC WES GC content
19 months ago
maria2019 • 30 • updated 19 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
19 months ago
maria2019 • 30 • updated 19 months ago
h.mon 25k
3
Votes
10
Replies
369
Views
How can I split WES FASTQ file into sub-files for each chromosome ?
WES split fastq chromosome
19 months ago
Laven9 • 0
1
Vote
0
Replies
190
Views
putative mosaic mutations
mosaic de novo wes sequencing
20 months ago
lait • 130
1
Vote
2
Replies
236
Views
Incorrect number of AD fields (2) at 1:878906 cannot merge
bcftools vcf WES
20 months 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
3.4 years ago
Irina Astrovskaya • 20 • updated 22 months ago
h.mon 25k
4
Votes
6
Replies
719
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
22 months ago
svlachavas • 560 • updated 22 months ago
finswimmer 11k
1
Vote
6
Replies
927
Views
Converting TCGA Bam files to fastq: Picard does not work!
wes sequencing
3.3 years ago
jonessara770 • 150 • updated 24 months ago
rmh1995 • 0
0
Votes
0
Replies
320
Views
Qs about mutect2
WES mutect2 gatk
2.0 years ago
walker • 20
0
Votes
3
Replies
274
Views
Enrichment platforms for 1000GP exome data
data WES
2.0 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
2.1 years ago
KumaraFM • 0 • updated 2.1 years ago
toralmanvar • 760
1
Vote
3
Replies
1.6k
Views
SciClone on WES data
sciclone wes clonality varscan dnacopy
3.5 years ago
mar.ark.parr • 30 • updated 2.1 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
4.4 years ago
felejohs • 70 • updated 2.1 years ago
zx8754 7.5k
1
Vote
1
Reply
374
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
2.1 years ago
jonessara770 • 150 • updated 2.1 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
2.3 years ago
miaowzai • 130 • updated 2.2 years ago
Biostar 20
0
Votes
1
Reply
415
Views
Database of Mutations and the associated drugs
WES ngs
2.2 years ago
Ron • 950 • updated 2.2 years ago
Kevin Blighe 43k
0
Votes
1
Reply
404
Views
CNV analysis from exome sequencing data
cnv wes
2.2 years ago
mkamranazim • 0
1
Vote
1
Reply
319
Views
Haplotype sharing of mutation carriers
ngs haplotype SNP WES
2.2 years ago
Lio04 • 0 • updated 2.2 years ago
Kevin Blighe 43k
1
Vote
3
Replies
373
Views
interpretation of intronic variant detected by WES
WES
2.3 years ago
jonessara770 • 150
0
Votes
1
Reply
256
Views
How to remove Variants where the Ref and Alt in the reference genome are switched?
NGS WES VariantCalling RefAlt
2.3 years ago
O.ibra • 0 • updated 2.3 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
2.3 years ago
svlachavas • 560
2
Votes
2
Replies
593
Views
How to take in consideration UMI in WES pipeline?
WES
2.4 years ago
jonessara770 • 150 • updated 2.4 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
2.4 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
2.5 years ago
maegsul • 140 • updated 2.5 years ago
chrchang523 5.2k
4
Votes
4
Replies
678
Views
sample mixing when demultiplexing
demultiplex WES human samples NGS BAM
2.6 years ago
lait • 130
0
Votes
4
Replies
504
Views
low coverage & BAF plots have three peaks
b-allele frequency low coverage WES human samples
2.6 years ago
lait • 130
0
Votes
1
Reply
461
Views
CNVkit segmetrics error
CNV WES germline
2.7 years ago
SPDouglas • 0 • updated 2.6 years ago
Eric T. ♦ 2.4k
0
Votes
8
Replies
613
Views
Create a custom exome .genome for IGV
IGV exome sequencing WES
2.7 years ago
jgarces • 10 • updated 2.7 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
3.2 years ago
a01039012387 • 10 • updated 2.7 years ago
nilesh.gardi2688 • 0
0
Votes
0
Replies
345
Views
High CG>CA and CG>TG errors from bait bias WES
WES bias
2.7 years ago
maduh17 • 10
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