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mskilab-org / fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing
MIT License
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CRAM support #11

Closed ppararaj closed 3 years ago

ppararaj commented 3 years ago

Hello, Thanks for the software. I was able to successfully run this on a several BAM files, but I was wondering if there are plans to include support for CRAM format?

I receive the following error when trying to run a CRAM file and looks like a modification of bamUtils will be required:

Error in bamUtils::bam.cov.tile(bam, window = as.numeric(window), chunksize = 1e+06,  :
  Cannot open BAM. A valid BAM for 'bam.file' must be provided.
Calls: fragCounter -> PrepareCov -> <Anonymous>
In addition: Warning message:
In readChar(check_gz, 4) :
  text connection used with readChar(), results may be incorrect
Execution halted
ShaiberAlon commented 3 years ago

Hi @ppararaj ,

Thank you for your interest in our tool. We don't currently have support for CRAM files and we don't have immediate plans to add this support (at least for now). What we do plan is to add an options for users to provide coverage counts from 3rd party tools and then just apply our GC and mappability correction (hoping to post updates here soon: #12 ). An (often superior) alternative to the coverage correction offered by fragCounter is using dryclean. Dryclean works well with uncorrected read depth counts.

There are many tools that offer fast coverage depth computations, for example: megadepth

If you are using fragCounter because you wish to use JaBbA, then you can use a tool of your choice for coverage depth calculation and supply that as input for JaBbA (with or without dryclean processing).

rdmorin commented 3 years ago

We're working with @mskilab on a meta-analysis of lymphomas. This is a show-stopper for us at the moment. Any thoughts on when this new functionality will become available?

mskilab commented 3 years ago

Hi Ryan- I think cram support should be pretty easy to implement. I think can have it by Monday?

Marcin

From: rdmorin @.***> Sent: Thursday, July 8, 2021 11:53 AM To: mskilab/fragCounter Cc: Marcin Imielinski Laboratory; Mention Subject: Re: [mskilab/fragCounter] CRAM support (#11)

We're working with @mskilabhttps://github.com/mskilab on a meta-analysis of lymphomas. This is a show-stopper for us at the moment. Any thoughts on when this new functionality will become available?

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rdmorin commented 3 years ago

That would be great. Thanks Marcin!

mskilab commented 3 years ago

hi all - just added cram support and pushed to master --> please give it a spin and let us know! You will need to reinstall mskilab/bamUtils as well. Best-Marcin

ppararaj commented 3 years ago

Hello, I've tested the new feature on a some GRCh37 CRAM files and it appear to work without issue. Thank you.

mskilab commented 3 years ago

Great

On Sat, Jul 10, 2021 at 12:12 PM Prasath Pararajalingam < @.***> wrote:

Hello, I've tested the new feature on a some GRCh37 CRAM files and it appear to work without issue. Thank you.

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