rebase 326 #330
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rebase 326 #330
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Avoids dependency of bpm to name allele B frequencies (abf) file.
to separate median idat intensity retrieval from verifyIDintensity bundled into contamination.smk
…cks with vcf entry
Modifis the entry_points.smk to create BCF entry point by simply converting BCF to plink BED. Testing and validation yet to be done.
A previous commit puts them in a separate idat_intensity.smk
Modifies contamination.smk and grouped_contamination.py to enable contamination check in cluster mode.
Avoids the dependency on IDAT files for calculating median intensity with VCF/BCF input. Adds scripts for both in per-sample and grouped/cluster mode. Modifies the intensity workflow to execute appropriately if VCF/BCF input.
…kefile and sample_qc subworkflow Other than existing 'use_contamination' checks, also adds 'intensity_retreived' and 'contamination_checked' tests which simply tests specifically if output csv files were created regardless of configs/entry point to feed them to sample_qc.
… check is default
Removes idat_intensity.smk and keeps intensity_check.smk
Renames from vcf_file to bcf_file explictly indicate that bcf is input.
snakemake params were imported through named import. Changed to import all params through a loop in unnamed fashion. Allows seemless compatibility when gtc or bcf entry point is used.
The starting few lines were duplicated in the entry_points in copy/paste. This removes the duplicated lines.
…r contamination checks. Previously GC_SCORE was added to the adpc.bin which had depenency that a cluster egt file had to be used in preparation of vcf/bcf. IGC score is encoded in gtc so doesn't depended on cluster egt file. The conamination scores should also be more similar with the gtc input.
Consistent with vcf2adpc.py. Now both should IGC and work with vcf/bcf prepared with gtc2vcf workflow.
…ontamatination.py
Earliar gentrain score was used to mark AF as NA if score is negative. This change excludes using it to ensure compatibility with gtc2vcf workflow prepared bcf.
…ing with BCF input.
…processing for both IDAT and BCF input.
BCF entry point with intensity and contamination checks using BCF for data_catalog usage.
carynwillis
changed the title
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Rebases issue_326 to default