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Why some of my diagram figs have extra genes in chr1? #579

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HYan-lei opened this issue Mar 16, 2021 · 7 comments · Fixed by #580
Closed

Why some of my diagram figs have extra genes in chr1? #579

HYan-lei opened this issue Mar 16, 2021 · 7 comments · Fixed by #580

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@HYan-lei
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Hi,

I run all the samples together. Most samples's diagram figs are normal, but few of them have extra gene names in chr1. I used the cnvkit cnvkit 0.9.7.b1. Can you please help me with this issue? Thanks. HY
19_BLE_65.diagram.pdf
@tskir
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tskir commented Mar 17, 2021

Hi @HYan-lei,

A number of plotting bugs were recently fixed in CVNKit version 0.9.8, and this one looks like it should be one of them. Could you please upgrade to the latest version and see if this resolves the problem?

@HYan-lei
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Thanks. I just tried the 0.9.8 version, and still has the same issue.

@tskir
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tskir commented Mar 18, 2021 •
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@HYan-lei You're right! It's a different one, I was able to reproduce it.

It turned out to have the same underlying reason as issues #573 and #576.

As a result, it will be fixed by the PR I just submitted, #580. I've tested that the changes actually do fix the chromosome diagram.

Thank you for reporting it!

@tskir tskir mentioned this issue Mar 18, 2021
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@tskir
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tskir commented Mar 18, 2021

Oh, and actually, the reason you're only seeing extra genes in chr1 is because the indexing function was broken for all chromosomes except 1. So with the fix, you will very likely see lots of extra genes for all chromosomes.

The actual reason you're seeing lots of extra genes is probably the samples themselves. In my experience, for every batch of samples (depending on technology, protocols etc.), there will be a small number of "noisy" samples which appear to have lots and lots of CNVs. This usually just means that the coverage profile for them is different from the rest of the batch.

This issue will close when the PR is merged, but if you continue to have problems, please do not hesitate to open a new one.

@HYan-lei
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What you mean "when the PR is merged?" Thanks.

@tskir
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tskir commented Mar 18, 2021 •
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This means I've submitted a code change which will fix this issue (#580), and it's now up to the author of CNVkit to review and merge (accept) it. Once this is done and the new version is released, the issue will be resolved.

@HYan-lei
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great. Thanks. I will try to run again when the new version is released. Thanks for the help.

@etal etal closed this as completed in #580 Apr 5, 2021
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Fix subgary indexing in cnary.by_gene() tskir/cnvkit
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@tskir @HYan-lei