Added lines to write vcftools commands to the log file
Fixed incorrect log file names on two line of ExmVC.4
Changed VCF header files to a table
Various changes in initial drafts of the annotation pipeline. Currently generates an annotated vcf for each individual but this splits multiple alternate alleles across multiple lines, which is not correct according to VCF4.2 specifications. Need to change this.
Added 1KG indel reference. Adjusted some allocations
Fixed paired-end detection bug
Added 1KG InDel reference. Changed final rm command.
Added 1KG indel reference and fixed DBSNP variable
Added 1KG indel reference
Changed output file name. Fixed input file path.
Added routine to change Info fields used depending on variant caller being used.
Various further changes in initial annotation pipe.