3.9.0 - Masking invalid complex INDEL calls

3.9.0

• Masking implemented to remove calls from pindel output where 'ref == alt'. These complex indel calls are invalid and were not present prior to 3.6.0 changes
  • Core pindel fix required to resolve the underlying problem

3.8.0 - New normal panel flag method (optional)

• Adds -noflag option to pindel.pl for use cases where flagging needs to be executed separately or not at all.
• Add -range option to pindel_np_from_vcf.pl
  • Creates bed.gz using pindel call range instead of legacy gff3.gz
• Adds new flag FF021, normal panel filtering using pindel call range
  • Legacy normal panel filtering remove variants with any overlap with normal panel, looses larger events that we have more confidence in with longer reads.
  • This is not included by default in any flag set
  • A different normal panel needs to be constructed to use this (bed.gz)
• Nextflow DSL2 worflows
  • pindel_pl - wraps pindel.pl, subworkflow included for later use.
  • np_generation - Generate a normal panel from a list of input BAMs
    • Handles the complete data generation and conversion to bed/gff3.

3.6.0 - new FFPE flags

New flag rule set pulldownFfpeRulesFragment.lst including FF019 and FF020 made

v3.5.0 - change to pindel core

Fix in underlying pindel algorithm to allow complex events with inserted sequence longer than the deleted element.

Causes a minor shuffle DI events which are known to be subjective.

v3.3.0 - IO hardening

See milestone 3

v3.2.0 - speedup

The input step (which runs pindel_input_gen.pl) is now significantly faster (~50% shorter run time).

There is no scientific impact from this change.

v3.1.2 - Species name command line fix

Resolves bug introduced in 3.0.5

v3.1.1 - Processing for mmQC processed BAMs

• Stable release for working with BAMs passed through mismatch QC
  • Works with data not handled in this way also
• Fix regression in 3.x branch affecting results with no events on individual chromosomes.

Hotfix v3.0.6

• Handles species names with spaces
• modified checks for species, assembly and checksum

v3.0.4 - bugfix - affects previous v3.0.x releases

A silent failure in the construction of pindel alignment BAM files was introduced in v3.0.0 resulting in file containing only a header.

This release fixes this bug.

We have updated our testing strategy to ensure this doesn't occur in future.