svtools v0.4.0

Major changes

• SVTyper has been updated to 0.7.0 which brings in improvements to genotyping quality, duplication sensitivity and speed improvements (courtesy of @brentp) for CRAM files.
• Support for 8-column VCFs.
• Introduction of a protocol for tiered-merging for very large cohorts via enhancements to svtools lmerge. Thanks to @abelhj.
• Multiple fixes to the classifier including manual specification of sex chromosomes which fixed a key bug when chromosomes were prefixed with a 'chr'.
• Fixes to svtools varlookup for bugs in parsing the INFO field.
• Fixed a major bug in svtools prune which occasionally resulted in incorrect results.
• Set the copynumber for the entire sample to -1 if CNVnator is unable to genotype the sample correctly. Previously svtools copynumber would die upon encountering a -1 which resulted in truncated files.
• Fixed a parsing bug in svtools vcftobedpe for BNDs on chromosomes containing a : in their name.

Minor changes

• Multiple documentation improvements.
• More helpful error handling in a number of situations.
• Better support for manta VCFs.