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7 votes
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Database of copy number alterations in different cancer types

I don't know if there's a database that does exactly what you want, but there are some places that might help you figure this out, especially if you already have a list of CNAs/genes/regions in mind. ...
Jared Andrews's user avatar
4 votes
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What does this statement mean?

They created 10kb bins, which could be called "dividing the genome". These are just 10kb long contiguous stretches (so position 1-10000,then 10001-20000, etc.). This is, of course, a nonsensical way ...
Devon Ryan's user avatar
  • 19.6k
3 votes

Method to detect genome doubling

In a tissue or cell line that used to be diploid and has undergone genome wide doubling, you expect more variants having observed allele frequencies that would also occur in tetraploid organism. That ...
Timur Shtatland's user avatar
3 votes
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Does GISTIC (v 2.0) estimate amplified/deleted probabilities on a single sample basis?

There doesn't seem to be much differences between GISTIC 1.0 and 2.0 as it says: As with GISTIC 1.0, we obtain P-values for each marker by comparing the score at each locus to a background score ...
llrs's user avatar
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3 votes
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Comparing two files with overlapping regions and get their associated information

You can use bedtools intersect and cut the results: ...
Devon Ryan's user avatar
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3 votes
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Compute copy number from cases and controls

GISTIC does exactly this, and is very possibly the tool used in your link above. The input files need to be in a different format than what you currently have, but if you're using a SNP6 array, ...
Jared Andrews's user avatar
2 votes

Database for germline copy number variations in cancer

You can find CNV (and other structural variant) information in: DECIPHER DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database ...
terdon's user avatar
  • 9,826
2 votes
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cn.MOPS fails with 'missing value where TRUE/FALSE needed'

I managed to track down what was producing this error. The problem was that my bed file only had one segment for chromosome chrUn_gl000228. However, the cn.MOPS ...
terdon's user avatar
  • 9,826
2 votes

Joining columns to a sorted file

Rearrange your text file into a sorted BED file: ...
Alex Reynolds's user avatar
2 votes
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VCF merge containing CNV

vcf-merge (or better: bcftools merge) does a column-based merge of VCF files, basically taking on an additional genotype column ...
gringer's user avatar
  • 13.9k
2 votes
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How to visualise the proportion of clonal genes to sub clonal genes

I've used some dummy data for simplicity. It's fairly easy to do this with ggplot, but you have to format your matrix-like data for ggplot input. eg : ...
RoB's user avatar
  • 146
1 vote

Calculating the number of probes for a given genomic range

Regardless of what your specific data is, the goal of your analysis is really to find overlaps between two data frames of genomic coordinations. My favorite package for doing this is GenomicRanges. It ...
Phoenix Mu's user avatar
1 vote
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CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`

Could you download it from conda and try again? Its here, https://docs.conda.io/en/main/miniconda.html Then, ...
M__'s user avatar
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1 vote
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GATK g CNV code Aborts Before Running Main Code

You are using ${CHROMOSOME_NAMES[@]} but you never define that, so when your code gets here: ...
terdon's user avatar
  • 9,826
1 vote
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what does ALT ID DUP refer to when ALT ID for copy number are already specified?

The details will depend on the specific tool used to generate the VCF. Each tool has its own system and there is not much standardization for these fields. That said, the likeliest situation here is ...
terdon's user avatar
  • 9,826
1 vote
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Definition of "proband" in CNV analysis

answer from @maximilian-press, converted from comments: https://www.genome.gov/genetics-glossary/Proband https://www.merriam-webster.com/dictionary/proband A proband is an individual affected with a ...
1 vote

A unified database for CNV, SNP, Indel and MSI

To Answer my own question, one can use variation viewer to get all the information :) DisGeNet is another resource.
Angelo's user avatar
  • 237
1 vote

polidy VCF file for Canvas somatic-wgs cnv calling

It seems you need to supply vcf files specifying the ploidy of the sex chromosomes. See https://github.com/Illumina/canvas/issues/89 for explanation and example vcf files.
Florian's user avatar
  • 11
1 vote
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Cromwell: can't find file ID

I updated to the newest version of Cromwell and the error went away!
Stephanie Hoyt's user avatar
1 vote

Method to detect genome doubling

The following may work, assuming you have an Illumina genome sequence library with decent coverage, preferably amplification-free: Use kat to produce a kmer spectrum plot of the reads (kmer abundance ...
Jay Moore's user avatar
  • 1,012
1 vote

Detection of CNV(InDel) of intermediate size

There is a trade off between read length and the limit of the indel that can be accurately mapped. Intermediate-size indels specifically are better detected with longer read lengths.
Husami's user avatar
  • 11
1 vote

Detection of CNV(InDel) of intermediate size

My impression is that small InDel (a couple of bp) is identified through cigar string in BAM... Well, yes, by gaps in the alignment, easily detected by examining the CIGAR string. ...and typical ...
Daniel Standage's user avatar
1 vote

Arm-level SCNA does not change mRNA expression level?

Answer from @devon-ryan, converted from comments: The common presumption in such cases is that there's a feedback loop on most genes to control their expression level. It doesn't have to be specific ...
1 vote

Save output to a specific folder and/or with a specific prefix in Cancer Genomics Cloud

If the output is File, you can add this step https://github.com/Barski-lab/workflows/blob/master/tools/rename.cwl to rename the output file.
Michael Kotliar's user avatar
1 vote

Simulate and test CNV workflow?

I cannot tell exactly from the post or the linked project what type of data these scripts are designed for, but I am going to assume that "Scripts involved in our workflow for detecting CNVs from WGS ...
winni2k's user avatar
  • 2,256
1 vote
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how to count the number of each allele of CNVs?

Here's a pure python solution to process your example. It should be straightforward to loop over all the rows of your vcf files ...
heathobrien's user avatar
  • 1,816

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