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questions
1
vote
1
reply
1.1k
views
lofreq empty output?
lofreq
updated 2.3 years ago by
whb
▴ 60 • written 3.9 years ago by
vctrm67
▴ 50
1
vote
4
replies
2.8k
views
Interpreting GISTIC2 output
GISTIC
updated 2.4 years ago by
MatthewP
★ 1.4k • written 3.5 years ago by
vctrm67
▴ 50
0
votes
2
replies
1.2k
views
HRD score LST?
cnv
updated 2.6 years ago by
e.rempel
★ 1.1k • written 3.5 years ago by
vctrm67
▴ 50
2
votes
1
reply
641
views
Getting sample IDs from dbGaP SRR?
dbgap
updated 3.2 years ago by
Biostar
20 • written 3.3 years ago by
vctrm67
▴ 50
0
votes
0
replies
521
views
Extract VCF of tumor variants from a list of SNPs
mutect2
SNP
3.3 years ago by
vctrm67
▴ 50
0
votes
6
replies
2.1k
views
CNVKit for unmatched tumor-only WGS samples
cnvkit
updated 13 months ago by
rohitsatyam102
▴ 840 • written 3.3 years ago by
vctrm67
▴ 50
0
votes
2
replies
1.1k
views
Mutect2 missing mutations
mutect
updated 3.4 years ago by
Ram
43k • written 3.4 years ago by
vctrm67
▴ 50
0
votes
0
replies
654
views
SV calling with duplication amplification
sv
3.5 years ago by
vctrm67
▴ 50
0
votes
3
replies
870
views
Amplification over deletion/Deletion over amplification?
gistic
updated 3.6 years ago by
Kevin Blighe
87k • written 3.6 years ago by
vctrm67
▴ 50
5
votes
3
replies
3.1k
views
bedtools sort doesn't properly sort
bedtools
updated 3.6 years ago by
Jorge Amigo
14k • written 3.6 years ago by
vctrm67
▴ 50
0
votes
0
replies
724
views
bedtools closest default?
bedtools
3.6 years ago by
vctrm67
▴ 50
3
votes
9
replies
1.4k
views
Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
CNV
3.6 years ago by
vctrm67
▴ 50
0
votes
7
replies
3.7k
views
GISTIC 2.0 for sequencing data
gistic
sequencing
wgs
cnv
cna
3.6 years ago by
vctrm67
▴ 50
1
vote
3
replies
980
views
Calling CNVs using a single tumor sample
cnv
3.6 years ago by
vctrm67
▴ 50
0
votes
0
replies
508
views
CNV segmentation purpose
cnv
3.6 years ago by
vctrm67
▴ 50
1
vote
4
replies
789
views
Detecting aneuploidy in sequencing data or copy number profile?
ngs
updated 3.6 years ago by
igor
13k • written 3.6 years ago by
vctrm67
▴ 50
0
votes
0
replies
587
views
ASCAT CN vs SNP probes
ascat
3.7 years ago by
vctrm67
▴ 50
0
votes
3
replies
2.2k
views
Calculating HRD score
HRD
updated 2.5 years ago by
Tsaousis
• 0 • written 3.7 years ago by
vctrm67
▴ 50
0
votes
1
reply
887
views
Number of probes per segment from ASCAT SNP array output?
ascat
3.7 years ago by
vctrm67
▴ 50
0
votes
4
replies
1.5k
views
TCGA CNV data reformatting
CNV
updated 3.7 years ago by
markus.riester
▴ 550 • written 3.8 years ago by
vctrm67
▴ 50
0
votes
1
reply
844
views
bcftools isec question?
bcftools
updated 3.9 years ago by
Pierre Lindenbaum
161k • written 3.9 years ago by
vctrm67
▴ 50
0
votes
5
replies
2.3k
views
Get nonoverlapping regions of two bed files
bed
3.9 years ago by
vctrm67
▴ 50
1
vote
5
replies
1.6k
views
Calling CNVs without a normal
CNV
updated 4.0 years ago by
Biostar
20 • written 4.2 years ago by
vctrm67
▴ 50
1
vote
7
replies
1.3k
views
Parallelizing GATK4 tools
GATK
4.0 years ago by
vctrm67
▴ 50
0
votes
1
reply
724
views
Rename "SM" tag in read group only
GATK
updated 2.7 years ago by
Lucy
▴ 140 • written 4.0 years ago by
vctrm67
▴ 50
0
votes
0
replies
1.2k
views
Calling germline SNPs using GATK HaplotypeCaller in a single sample
GATK
4.0 years ago by
vctrm67
▴ 50
0
votes
1
reply
544
views
Why are BED files necessary for somatic calling?
somatic
4.1 years ago by
vctrm67
▴ 50
1
vote
7
replies
1.3k
views
Get intersection of files occuring in at least 2 files?
bedtools
updated 4.1 years ago by
Alex Reynolds
35k • written 4.1 years ago by
vctrm67
▴ 50
0
votes
8
replies
1.7k
views
Mutect output for CNV calling
cnv
updated 4.1 years ago by
Biostar
20 • written 4.2 years ago by
vctrm67
▴ 50
0
votes
7
replies
4.7k
views
Bcftools unsorted positions?
bcftools
4.2 years ago by
vctrm67
▴ 50
4
votes
4
replies
1.0k
views
Replacing BAM reference
bam
updated 4.2 years ago by
swbarnes2
14k • written 4.2 years ago by
vctrm67
▴ 50
0
votes
1
reply
1.1k
views
CNVKit interpretation of results?
cnvkit
updated 4.2 years ago by
jared.andrews07
★ 16k • written 4.2 years ago by
vctrm67
▴ 50
0
votes
3
replies
775
views
Annovar produces uncalled mutations?
annovar
updated 4.2 years ago by
Kevin Blighe
87k • written 4.2 years ago by
vctrm67
▴ 50
0
votes
0
replies
610
views
Eliminating panel mutations based on coverage of PoN
GATK
filtering
4.3 years ago by
vctrm67
▴ 50
0
votes
1
reply
687
views
GATK BaseRecalibrator and platform?
gatk
4.3 years ago by
vctrm67
▴ 50
1
vote
5
replies
1.2k
views
Hg19 version based on bam file contigs?
hg19
4.3 years ago by
vctrm67
▴ 50
3
votes
10
replies
3.0k
views
Illumina WES intervals file for coverage analysis?
illumina
updated 4.3 years ago by
trausch
★ 1.9k • written 4.3 years ago by
vctrm67
▴ 50
0
votes
1
reply
1.1k
views
Samtools for corrupt bam?
samtools
4.3 years ago by
vctrm67
▴ 50
1
vote
1
reply
2.0k
views
Using Bedtools coverage to find BAM coverage?
bedtools
written 4.5 years ago by
vctrm67
▴ 50
0
votes
0
replies
814
views
Sequenza gives sequence not found error?
sequenza
updated 4.3 years ago by
Biostar
20 • written 4.5 years ago by
vctrm67
▴ 50
0
votes
4
replies
1.1k
views
Annovar in hg19 mode
annovar
4.4 years ago by
vctrm67
▴ 50
0
votes
1
reply
1.7k
views
LiftOver from b37
liftover
updated 4.4 years ago by
Pierre Lindenbaum
161k • written 4.4 years ago by
vctrm67
▴ 50
2
votes
5
replies
2.1k
views
Bcftools concat gives chromosome contiguous error?
bcftools
4.5 years ago by
vctrm67
▴ 50
3
votes
1
reply
2.8k
views
Hg38 to b37 LiftOver chain?
picard
4.5 years ago by
vctrm67
▴ 50
0
votes
1
reply
1.4k
views
Using GATK AddOrReplaceReadGroups
GATK
updated 4.5 years ago by
Pierre Lindenbaum
161k • written 4.5 years ago by
vctrm67
▴ 50
0
votes
0
replies
1.0k
views
How to use CNVKit
cnvkit
4.5 years ago by
vctrm67
▴ 50
1
vote
1
reply
617
views
Combine samples in bam/vcf
GATK
updated 4.5 years ago by
Pierre Lindenbaum
161k • written 4.5 years ago by
vctrm67
▴ 50
0
votes
2
replies
1.0k
views
Error when unzipping .gz files from GATK?
GATK
updated 4.5 years ago by
Ram
43k • written 4.5 years ago by
vctrm67
▴ 50
0
votes
3
replies
1.6k
views
Combining two VCFs each with own set of mutations
vcf
updated 4.5 years ago by
jared.andrews07
★ 16k • written 4.5 years ago by
vctrm67
▴ 50
2
votes
4
replies
1.4k
views
Comparing calls from different VCFs
vcf
maf
4.5 years ago by
vctrm67
▴ 50
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