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: somatic • reset
0
votes
3
replies
348
views
Germline variant - should it be seen in the somatic vcf?
vcf somatic
updated 8 weeks ago by 44k • written 8 weeks ago by ▴ 190
6
votes
2
replies
6.4k
views
Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
CNV somatic facets cancer
8 weeks ago by dariober 15k
1
vote
2
replies
329
views
Germline and somatic SNPs in same or different allele
germline vcf phasing somatic
8 weeks ago by Nacho del Valle • 0
2
votes
2
replies
403
views
Somatic Variant Calling from Nanopore Data
variant somatic calling cancer nanopore
updated 10 weeks ago by 146k • written 10 weeks ago by ▴ 50
0
votes
0
replies
188
views
Consistent somatic CNV calling across samples: spurious, error or real?
MANTA CNVKit SV somatic CNV
updated 12 weeks ago by 146k • written 12 weeks ago by ▴ 30
0
votes
2
replies
269
views
Seeking Opinions on Pipeline for Detecting Somatic Variants and Rare Germline Mutations
snps germline somatic gatk
12 weeks ago by George ▴ 10
0
votes
0
replies
168
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
6 months ago by feather-W • 0
0
votes
0
replies
301
views
Issues while trying to create my own PON (Panel Of Normals) with GATK
vcf gatk somatic genomics variants
7 months ago by Samuel ▴ 20
1
vote
3
replies
565
views
Can't use VarScan2 to call somatic variants from my tumor/sample vcf pair
mutations vcf somatic varscan2 samtools
updated 7 months ago by 164k • written 7 months ago by ▴ 20
0
votes
2
replies
552
views
Problem merging plink files for somatic variants.
plink somatic vcf
7 months ago by Palgrave ▴ 130
4
votes
2
replies
612
views
How can I know if a gene mutation is somatic or germline?
somatic mutation germline
updated 9 months ago by 4.5k • written 9 months ago by • 0
1
vote
1
reply
360
views
Searching for a specific somatic mutation in Illumina data
somatic Illumina
updated 9 months ago by ★ 1.5k • written 9 months ago by ▴ 20
5
votes
1
reply
648
views
Detecting somatic variants in non-tumor tissue without normals
somatic brain tumor
9 months ago by manfi ▴ 20
5
votes
6
replies
1.1k
views
Inquiry Regarding Somatic Analysis and Normal Sample Requirement
ngs somatic germline
updated 17 months ago by 44k • written 17 months ago by ▴ 50
0
votes
0
replies
377
views
Anyone familiar with ICGC's DCC data releases?
cancer TCGA PCAWG ICGC somatic
19 months ago by ConvolutedGenome ▴ 50
9
votes
2
replies
1.1k
views
Somatic truth set
benchmarking Somatic
updated 19 months ago by ▴ 160 • written 19 months ago by ▴ 260
5
votes
1
reply
617
views
How to identify whether the sample is from only one person and whether the sample is tumor or normal
somatic NGS
updated 20 months ago by 85k • written 20 months ago by ▴ 10
0
votes
1
reply
516
views
Novogene somatic results with GATK mutect2
Mutect2 Novogene GATK somatic VCF
updated 21 months ago by 146k • written 21 months ago by ▴ 20
0
votes
0
replies
415
views
How quality score for somatic mutations in ICGC was calculated
somatic mutations ICGC
21 months ago by caochch • 0
3
votes
2
replies
1.3k
views
Mutect2 read orientation bias filter effect on Somatic variant calling
somatic bias orientation mutect2
22 months ago by asalimih ▴ 60
7
votes
2
replies
893
views
genotypes - somatic data
genotype caller data somatic variant
updated 23 months ago by 4.9k • written 23 months ago by ▴ 20
1
vote
1
reply
508
views
Complex somatic variants database
somatic structural variants
updated 24 months ago by 164k • written 24 months ago by • 0
0
votes
0
replies
427
views
WGS trimming end of the reads for specific bp before alignment and call somatic variants
read trim WGS somatic variant
2.0 years ago by woongjaej ▴ 30
0
votes
0
replies
416
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq somatic Variant-calling germline
updated 7 months ago by 44k • written 2.0 years ago by • 0
0
votes
2
replies
598
views
Is there a way to call somatic mutations from methylation sequencing data？
methylation data mutation sequencing somatic
2.0 years ago by yang • 0
2
votes
1
reply
1.7k
views
Get both somatic and germline mutations from tumor only sample?
germline gatk somatic mutect2 gnomad
updated 2.2 years ago by ★ 1.5k • written 2.2 years ago by ▴ 10
7
votes
14
replies
2.8k
views
7 follow
Forum: Why isn't GWAS used in oncology?
gwas association oncology studies somatic cancer
updated 2.2 years ago by 4.3k • written 2.2 years ago by ▴ 90
2
votes
5
replies
1.1k
views
is there any pipeline or best practices of detecting germline neoantigen?
somatic pipeline neoantigen germline
2.3 years ago by likeabboo • 0
2
votes
1
reply
736
views
somatic SNV tool for ONT samples
somatic ont SNV
updated 2.4 years ago by 4.5k • written 2.4 years ago by ▴ 10
0
votes
0
replies
356
views
ion torrent oca data analysis using gatk for somatic mutations
somatic mutact2 iontorrent
2.4 years ago by sskimvd • 0
0
votes
0
replies
465
views
Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
2.5 years ago by whb ▴ 60
0
votes
1
reply
650
views
why Mutect2 calls some germline variants as somatic ones?
somatic germline haplotypecaller mutect2
updated 2.7 years ago by ★ 1.5k • written 2.7 years ago by ▴ 280
0
votes
0
replies
560
views
how to visually compare BAM file differences
mutation tumor GATK bam somatic
2.9 years ago by tan ▴ 10
11
votes
8
replies
3.7k
views
Base recalibration in normal vs. tumor somatic variant calling in WXS data?
WXS recalibration variant somatic
updated 14 months ago by ▴ 70 • written 3.0 years ago by ▴ 60
0
votes
0
replies
529
views
How to compare and group samples according to common mutated genes in R
variants rstudio somatic samples grouping
3.1 years ago by Camilo Andres ▴ 40
2
votes
2
replies
1.1k
views
mixing hg38 and GRCh38 during variant calling
somatic GATK WES NGS
3.1 years ago by yaro ▴ 10
0
votes
1
reply
630
views
How is better perform the analyze the somatic mutations? (the mutations of my interest gene)
somatic VCF annotation Oncoplot
updated 3.1 years ago by ★ 2.9k • written 3.1 years ago by • 0
7
votes
6
replies
1.6k
views
Can non-driver mutations disrupt the function of proteins and further affect a cellular pathway?
driver somatic annotation VCF oncoplot
updated 3.2 years ago by ▴ 1000 • written 3.2 years ago by ▴ 110
6
votes
8
replies
2.6k
views
Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?
mutation low WGS lcWGS pipeline somatic coverage calling
updated 3.2 years ago by 6.1k • written 3.2 years ago by ▴ 30
1
vote
3
replies
1.5k
views
Validation of somatic variant calling pipeline
calling somatic validation variant
updated 3.2 years ago by 22k • written 3.2 years ago by • 0
4
votes
3
replies
1.1k
views
somatic short variant calling from patients having autoimmune disease
somatic immunedisease gatk variant
3.2 years ago by Mehmet ▴ 820
0
votes
0
replies
597
views
somatic variant calling with Mutect2
calling somatic Mutect2 variant
3.3 years ago by Elisa • 0
1
vote
1
reply
1.3k
views
GenomicsDBImport from Mutect2 output
Mutect2 GenomicsDBImport somatic VCF GATK
updated 16 months ago by ▴ 100 • written 3.3 years ago by ▴ 280
12
votes
9
replies
5.3k
views
Good annotation databases for a VCF file (somatic variants)
VCF ANNOVAR somatic databases annotation
updated 3.3 years ago by ▴ 130 • written 3.4 years ago by ▴ 110
0
votes
1
reply
818
views
Detection of biallelic mutation (inactivation)
somatic biallelic mutation
updated 3.4 years ago by ▴ 160 • written 3.4 years ago by ▴ 750
0
votes
1
reply
746
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 3.5 years ago by ▴ 580 • written 3.5 years ago by ▴ 430
0
votes
0
replies
570
views
drug resistance informations for variations
cosmic somatic drug variants germline
3.5 years ago by enes ▴ 40
0
votes
0
replies
853
views
panel of normals for mutect2
mutect2 gatk NGS PoN somatic
3.5 years ago by lait ▴ 180
0
votes
0
replies
1.2k
views
germline vs somatic CNV GATK calling
CNV germline somatic GATK WGS
3.6 years ago by cocchi.e89 ▴ 280
0
votes
2
replies
988
views
somatic variant calling
variant calling somatic unpaired
updated 3.7 years ago by ▴ 350 • written 3.7 years ago by ▴ 20
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