Entering edit mode
7.5 years ago
Floris Brenk
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1.0k
Hi all,
Is there an easy way (or software that does this) to identify chromosome abnormalities from WGS data? We have some WGS data of a few cell lines and want to check whether they are still OK. Or is the normal way just plotting the DP value (Approximate read depth) against the chromosome position?
What do you mean by abnormalities, indels or CNVs or beak-points; or is yours methylation data?
There are many available tools/pipelines in-case you want to look into structural variants or CNVs in particular - MetaSV, Varscan2, SVMerge, Numpy, CNVnator... If breakpoint specific - GRIDSS, breakseq... For methylation data Metilene.
This is WGS data, so I have a g.vcf file only... So most of the mentioned software packages dont work I guess
How was the data generated?
Illumina reads about 30x average coverage...
Then you probably also have access to the bam file?
Here you can find many many tools for structural variants in WGS: https://omictools.com/structural-variant-detection-category
No because of space issues I only got the g.vcf unfortunately...
Ough. That's not good. It's really not okay to delete original data. Or do you still have the fastq files?
I'm not aware of any tools working on (g.)vcf files for detecting chromosomal abnormalities.
I don't think you can find much from only VCF-files unless you write some pipeline yourself. Most of these tools use bam-files to understand CNVs and breakpoints. With 30X data you should just re-map and run onf of those.