Support WGS filtering in the preprocessing pipeline #46
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use bgzip
…deeprvat into feature/wgs-preprocessing
…deeprvat into feature/wgs-preprocessing
commit 101feb2 Author: Marcel Mück <mueckm1@gmail.com> Date: Tue Apr 9 11:56:54 2024 +0200 Annotations new features (#54) * added all changes from annotation-speedups branch * added gtf and genotype mock file for github tests * Delete example/annotations/preprocessing_workdir/preprocessed directory * Update annotation_colnames_filling_values.yaml * Corrected fill values for maf columns * Changed protein_id merging and exon distance filtering, s.t. no annotations are dropped * included rulegraph instead dag * based on suggestions from @endast * added version info for rockdb.yaml file * updated rulegraph Updated Documentation corrected nonfunctional links * added support for X/Y chromosomes, removed dependency on pvcf file * excluded mkl version 2024.1.0 since it is crashing pytorch(pytorch/pytorch#123097) * changed way file stems are assumed to include 'double ending' on input files. * removed unused lines, removed pvcf from config file * changed if statement for gene_id_file --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
commit ae5c83e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon Apr 15 11:01:03 2024 +0200 fixed bugs in the annotation pipeline based on issues #61, #62 and #63. (#64) * fixed bugs in the annotation pipeline based on issues #61, #62 and #63. * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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What
This PR adds support for filtering WGS data in the preprocesing pipeline using a gtf file.
we use
convert2bedbedtools slopand get_features.plTesting
TBD
Test scenarios
TBD