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User: vctrm67

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vctrm67 • 10
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Posts by vctrm67

<prev • 105 results • page 1 of 11 • next >
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Amplification over deletion/Deletion over amplification?
... I am running GISTIC on some modified ASCAT copy number profiles. Part of the algorithm is a deconstruction/reconstruction of the copy number profile to find statistically likely underlying somatic copy number alterations. The output is a structure Q that is described as: ``` The Qs structure added ...
gistic written 1 hour ago by vctrm67 • 10
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Comment: C: GISTIC 2.0 markers
... Do you know of any other programs that would work with CNV profiles derived from sequencing data, as opposed to array data? ...
written 4 days ago by vctrm67 • 10
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Comment: C: GISTIC 2.0 markers
... Hi Kevin, Just revisiting this because I am facing a similar problem. It seems GISTIC 2.0 still requires a segmentation file, which takes in a "Num Markers" field. Do you know how to address this if we are using sequencing data? ...
written 9 days ago by vctrm67 • 10
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bedtools closest default?
... I'm confused about the default behavior of `bedtools closest`. I ran the command `bedtools closest -a a.bed -b b.bed -k 1 > closest.bed` and got this as a part of the output (the columns correspond to chrom, start in `a.bed` and chrom, start in `b.bed`): ``` 9 5819608 9 5819608 9 5819608 9 6080 ...
bedtools written 11 days ago by vctrm67 • 10
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bedtools sort doesn't properly sort
... When I run bedtools sort, I get the following: ``` 1 3587786 3593830 DUP 1 8750767 8828371 DEL 1 36370717 36398152 DUP 1 37116380 37129915 DUP 1 162941074 163012466 DUP 1 221854550 221874415 DUP 1 225906937 225913690 DUP 1 242796286 242812227 DUP 1 247955111 248002324 DUP 10 29644179 29717839 DUP ...
bedtools written 12 days ago by vctrm67 • 10 • updated 2 days ago by Jorge Amigo ♦ 12k
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Comment: C: GISTIC 2.0 for sequencing data
... I do not know which software. Is that necessary? What does your script put for Num Markers instead? ...
written 15 days ago by vctrm67 • 10
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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... My mistake. I thought the distinction was SNPs are found within a certain percentage of the population, whereas germline SNVs could still be below that percentage. ...
written 16 days ago by vctrm67 • 10
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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... What about germline SNVs (not SNPs)? ...
written 16 days ago by vctrm67 • 10
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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... When you say "With somatic, you do not", so it is because of tumor purity and clonality that deviate this? ...
written 16 days ago by vctrm67 • 10
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Comment: C: Somatic SNVs vs. Germline SNPs for allele-specific copy number analysis
... But wouldn't it be better to use both somatic SNVs and germline SNPs even still? ...
written 16 days ago by vctrm67 • 10

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