Expose additional parameters for tweaking ensemble calling
Expose additional parameters for tweaking ensemble calling
Ensure variantcaller configuration order remains stable during parallel calling. Use first configured caller for base set of combination calls
Only write finalization information for combination configuration notes, not comparisons
Add in freebayes defaults suggested on mailing list
Allow additional classification parameters and generalize usage in input YAML config
Pass BAM file to annotation of non-GATK input files, otherwise we miss most metrics
Apply annotation only to combination recall items used in classification
Use local temporary directory during processing to avoid global tmp space issues
Use recommended freebayes min-alternate-fraction for diploid calling only
Avoid additional filtering with samtools which has filtering baked as part of standard calling pipeline
Downsample large whole genome input files during base quality recalibration to avoid long run times
Use snpEff annotated VCF file directly, removing dependency on old version and GATK annotator
Generalize snpEff data library retrieval to avoid hardcoding version names for Ensembl
Move config_load to more generic namespace to reflect new functionality
Update GATK and snpEff to use generalized retrieval of resources from configuration file
Avoid writing program id with new Picard 1.82 release, since tags are not supported by pysam parser
Provide direct splitting of input BAM files into fastq parts for distributed alignment, for avoiding multiple IO steps on large files
Avoid named pipes when splitting, use temporary files to ensure correct pysam reading
Default back to splitting through unix pipes. Correctly pull split numbers for existing split fastq files