Does Sarek currently use asmultipcf for ascat if m...
# sareka
Alexander Chang
09/04/2024, 2:36 PMDoes Sarek currently use asmultipcf for ascat if multiple samples from the same patient are detected?
Edith M. Ross, Kerstin Haase, Peter Van Loo, Florian Markowetz, Allele-specific multi-sample copy number segmentation in ASCAT, Bioinformatics, Volume 37, Issue 13, July 2021, Pages 1909–1911, https://doi.org/10.1093/bioinformatics/btaa538
asmultipcf is part of the ASCAT R package from version 2.5 onwards. The asmultipcf function contains a parameter to select whether the exact or the fast algorithm should be run, as well as an option to include the per-sample breakpoint refinement. Furthermore, samples can be weight adjusted to account for quality differences in the data. The manual contains example use cases, including a comparison to HATCHet (Zaccaria and Raphael, 2018).
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Rike Hanssen
09/04/2024, 2:45 PMno
Rike Hanssen
09/04/2024, 2:45 PMbut would be great to have
a
Alexander Chang
09/04/2024, 2:50 PMok let me take a look to see if I could help implement it, I'
party dino 2
Alexander Chang
09/04/2024, 2:50 PMm working with cancer phylogeny problems and this is one.
g
George Seed
09/04/2024, 2:57 PMasmultipcf for joint cnv calling would be fabulous.
a
Alexander Chang
09/04/2024, 5:40 PMany tips on how to test it? I've made a bunch of changes in the module and subworkflows but I'm not familiar with nextflow testing.
Alexander Chang
09/04/2024, 5:42 PMI dont' see a test_ascat.yml that I could use as a basis
Alexander Chang
09/04/2024, 7:38 PMnvm i figured it out
Alexander Chang
09/04/2024, 8:20 PMsubmitted the PR request, gonna need some help with the test draft I wrote though, I got confused how to access the bam files mentioned.
Alexander Chang
09/04/2024, 11:12 PMjust for my own future reference, is there a guide on how to run the tests?
I kept getting this error
ERROR ~ ERROR: Validation of 'input' file failed!
-- Check '.nextflow.log' file for details
The following errors have been detected:
* -- Entry 1 - crai: the file or directory 'HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai' does not exist.
* -- Entry 2 - crai: the file or directory 'HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai' does not exist.
* -- Entry 1 - cram: the file or directory 'HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram' does not exist.
* -- Entry 2 - cram: the file or directory 'HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram' does not exist.
s
Simon Pearce
09/07/2024, 9:41 AMASCAT itself still needs migrating over to nf-test, if anyone feels like a challenge
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