Error when converting AnnotSV TSV to VCF (single sample)

Question

Error when converting AnnotSV TSV to VCF (single sample)

wwgordon opened this issue 9 months ago · 10 comments

Hello,

This is another issue relating to the AnnotSV -> variantconvert handoff for VCF creation. I have created an issue in the variantconvert github and am linking it here in case the issue is arising from AnnotSV.

Essentially, I am having difficulty converting AnnotSV TSV output for a single sample to a VCF using variantconvert. From what I can tell, the TSV looks OK, but I am consistently getting the following error when trying to convert:
ValueError: When using an AnnotSV file generated from a VCF, all samples in Samples_ID column are expected to have their own column in the input AnnotSV file.

Thanks for all of your help and work!
William

Answer 1 · 2024-02-05T19:07:54.000Z

This bothers me a lot, but I don't have the skills to debug this. It's really specific to variantconvert.
Thank you for creating the variantconvert issue.

Answer 2 · 2024-03-07T10:37:03.000Z

Hi, I am facing the same problem and I have just written a comment in the issue opened at variantconvert github. I actually think there is a bug in AnnotSV as the root of the problem is the TSV file generated by AnnotSV. I am using single sample vcfs as input, but the TSV generated by AnnotSV has missing values for some cells of the "Samples_ID" column:

It seems that variantconvert needs those values to be present to generate the VCF. If I manually modify the TSV reported by AnnotSV by writing "SAMPLE" in every cell under the column "Samples_ID", variantconvert is able to generate the VCF.

So, I think the question is why AnnotSV is not including the sample ids for some entries in the reported TSV.

Edit: I've just seen an open issue about this here #180

Answer 3 · 2024-03-11T08:24:25.000Z

So, I think the question is why AnnotSV is not including the sample ids for some entries in the reported TSV.

If the GT is 0/0 for a given sample, AnnotSV does not report the sample name in the Samples_ID column.

--
cf README:

FYI 1)
Samples_ID: List of the samples ID for which the SV was called (according to the SV input file)

FYI 2)

FYI 3)

Answer 4 · 2024-03-12T10:35:46.000Z

@lgmgeo thanks for the answer, now its clear for me.

Answer 5 · 2024-03-19T14:29:23.000Z

Hi, Has the bug in variantconvert been fixed yet?

Answer 6 · 2024-03-19T14:31:41.000Z

The developer is working on it but I don't dare give a deadline...

Answer 7 · 2024-04-19T09:04:13.000Z

variantconvert version 2.0.0 is posted.
This should fix the bug.
I'm going on vacation this evening. I'll take care of it when I get back.

Answer 8 · 2024-05-06T13:50:19.000Z

AnnotSV 3.4.1 is posted with an updated version of variantconvert (v2.0.1).

Can you confirm that this fixes your bug?

Answer 9 · 2024-05-06T13:58:44.000Z

Thanks! I will check

Answer 10 · 2024-05-07T00:02:50.000Z

Tested and working on my end. Thank you!