Name change and a adjustements to the annotation script: add SnpEff annotations, add option for full Cadd annotation, add Cadd phred-scaled scores to annotation, add GATK annotations to ensure we have everything - for some reason not all of the rs IDs were coming through from dbsnp during variant calling.
Fixed up error checking for RG header information
Increased time allocation. Added a vcf output name option.
Added vcf name option
Added vcf name option. Changed name of next script in pipeline.
Changed name of next script in pipeline.
Changed counting of alleles - previously counting 0/0, 0/1, 1/1 and therefore ignoring multiallelic variants, changed. Also change tabs to spaces.
Added SnpEff jar
Tabs to spaces. Added SnpEff warning to gatklog clean up.
Change of name