8000 Provide reference files for WES for ASCAT · Issue #100 · nf-core/sarek · GitHub
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maxulysse opened this issue Jan 27, 2020 · 12 comments
Open

Provide reference files for WES for ASCAT #100

maxulysse opened this issue Jan 27, 2020 · 12 comments
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@maxulysse @SusiJo
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@maxulysse
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Issue by @Anuragksingh, moved from SciLifeLab#763

Hello,
I had some doubts over ascat.
It would be really helpful if you can provide some insights about that.

Can we use the available ascat directly on WES data?
I guess the creation of BAF and LogR files from bam would be same for WES data also.
Or do we need to apply additional filters to use ascat on WES data?
For reference kindly see this link:
VanLoo-lab/ascat#19
Also does we need to add --exome flag when running ascat on WES data?

Any suggestions on above aspects would be really helpful.

Thanks

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@maxulysse

Running ASCAT for WES is definitively something that we're thinking about.
I remember reading about this link before, I'll definitively look more into it.
Thanks again for all your interest in this project

@szilvajuhos

To run ASCAT on exome you will need a separate file of SNPs that is covering the targeted exons only

@dingxm

Hi,
We are trying to analyze exome data for copy number.
The exome data has extended probes covering regions outside of the exomes.
It seems that last year ASCAT could not use exome data without pre-processing, is this still true or is there a version that deals with Exome data now?
Thank you

@szilvajuhos

Hej,
If you have a BED file that is covering your WES target, I would recommend to make a .loci file i.e. by filtering the latest dbSNP for common biallelic SNPs that are overlapping your target.
You have to have quite a few loci positions (since the target is smaller and the genome is not covered evenly) to make sure you will still have enough SNPs.
@malinlarsson is better in playing with it, the .loci file I have created contains ~16M lines:

$ wc -l dbSNP_151_S04380110_AllExonV5_hg38.loci
16200625
$ head -3 dbSNP_151_S04380110_AllExonV5_hg38.loci
chr1    65529
chr1    65552
chr1    65591

We have managed to make meaningful charts with this loci file (I can share it if you want to give a try), but certainly it is only the beginning of finding the right settings.
@maxulysse maxulysse self-assigned this Jan 27, 2020
@maxulysse maxulysse added the enhancement New feature or request label Jan 27, 2020
@maxulysse maxulysse added this to the 3.0 milestone Aug 31, 2020
@SusiJo SusiJo mentioned this issue Jun 24, 2022
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@SusiJo
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SusiJo commented Jun 24, 2022

Hi,
this might be also of interest: The developers of Ascat recommend to use the Battenberg reference files for WES and explain how they can be created see here.

@FriederikeHanssen
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So this issue is halfway addressed (see #606 ). It is possible now to use ASCAT with WES, however, we are currently not providing the necessary reference files:

Reanme: Provide ASCAT WES reference files for GATK.GRCh38

@FriederikeHanssen FriederikeHanssen changed the title Improving WES with ASCAT Provide reference files for WES for ASCAT Jul 1, 2022
@FriederikeHanssen
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Will move this to backlog, we can provide the references in 3.1

@FriederikeHanssen FriederikeHanssen modified the milestones: 3.0, 3.1 Jul 1, 2022
@maxulysse maxulysse moved this to Backlog in Sarek Board Jul 22, 2022
@maxulysse maxulysse modified the milestones: 3.1, 3.2 Nov 23, 2022
@FriederikeHanssen
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On a good way with this new beautiful documentation #981

@maxulysse maxulysse modified the milestones: 3.2, 3.3 Jun 22, 2023
@FriederikeHanssen
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I am unsure whether it actually makes sense to provide these files. Do all manufucatures use the same coordinates in their kits? Otherwise I think we should rather aim for making the generation as straight forward as possible

@maxulysse maxulysse modified the milestones: 3.3, 3.4, 3.5 Feb 8, 2024
@alexanderchang1
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Hi, just wanted to follow up on this. Does Sarek currently allow ASCAT on WES only data?

@FriederikeHanssen
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Do you mean when there is no matched normal?

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@szilvajuhos
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szilvajuhos commented Jul 31, 2024 via email

@alexanderchang1
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Hi, I have matched normal, and already ran Sarek with the -wes option turned on with the matched normal, I just want to know how much i can trust the output, there were some github issues mentioned above which implied that Sarek may or may not be providing the correct .bed reference.

@szilvajuhos
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szilvajuhos commented Aug 5, 2024 via email

@FriederikeHanssen
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To add to @szilvajuhos answer: here some commands to help you construct the loci file for your kit

@FriederikeHanssen FriederikeHanssen removed this from the 3.5 milestone Aug 19, 2024
@alexanderchang1
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Hi, thanks, I will give this a shot.

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