New ad hoc to finish off stuck alignment steps
Changed to using samtools for merge as seems to be faster than Picard and handles the RGs in the header properly
No change, just uncommented step commmand
Added seqtk command to convert old phred+64 fastq format to phred+33 format with F flag
Added KillFile flag
Added options to omit original quality scores and unmapped reads from the output bam. Helpful if smaller bams preferred, not suitable for archiving
Added option to fix mis-encoded quality scores during variant calling. Also removed pipeline option as this is now the end of the mapping pipeline rather than the beginning of the variant calling pipeline
No change
Update annovar database directory
Change to error logging function