Update BAM/CRAM/VCF omit pattern defaults?

[mikkonie]

There has been discussion with @Nicolai-vKuegelgen on possibly updating the default BAM/VCF omit patterns. The ones used as default should IMHO be the most generally applicable possible. I'm not the expert here, so feedback is definitely welcome.

Current Defaults

• BAM/CRAM: *dragen_evidence.bam
• VCF: *cnv.vcf.gz, *ploidy.vcf.gz, *sv.vcf.gz

Suggested Replacements

• BAM/CRAM: *GRCh38*
• VCF: *delly2*.vcf.gz, *manta*.vcf.gz, *melt*.vcf.gz, *gcnv*.vcf.gz, *GRCh38*

Comments or other suggestions?