4.0.8.0
This release features some significant changes to Mutect2
that improve both performance and correctness, as well as a bug fix to GenomicsDBImport
for large interval lists.
As usual, a docker image for this release can be downloaded from https://hub.docker.com/r/broadinstitute/gatk/
Full list of changes in this release:
-
Mutect2
- Handle overlapping mates in M2 active region detection, causing fewer false active regions (#5078)
- Makes Mutect2 ~25% faster in many cases with no loss of accuracy!
- Filter M2 calls that are near other filtered calls on the same haplotype (#5092)
- A very effective new filter that significantly reduces false positives
- New Orientation Bias Filter (#4895)
- New, improved orientation bias model, without which the M2 pipeline is not viable for NovaSeq data.
- Changed the default AF slightly for M2 tumor-only mode (just a small tweak) (#5067)
- Optimize some Mutect-related tools (#5073)
- Everything that inherits from
AbstractConcordanceWalker
(this includes theConcordance
tool andMergeMutect2CallsWithMC3
) is now much faster on the cloud
- Everything that inherits from
- Fixed edge case for M2 palindrome transformer (#5080)
- Fixed an edge case involving reads assigned huge fragment lengths
- Allowing counts for supporting alt reads in the validation normal. (#5062)
- Added useful information suggesting possible normal artifacts in somatic validation tool.
- M2 wdl doesn't emit unfiltered vcf, which is redundant (#5076)
- Handle overlapping mates in M2 active region detection, causing fewer false active regions (#5078)
-
GenomicsDBImport
-
Updated
MarkDuplicatesSpark
tie-breaking rules to reflect changes in picard (#5011) -
Added the ability for
CompareDuplicatesSpark
to output mismatching reads (#4894) -
Updated our
google-cloud-java
fork to 0.20.5-alpha-GCS-RETRY-FIX (#5099)- We now retry on 502 and UnknownHostException errors when using NIO
-
SV Tools
:- Various improvements (#4996)
- output a single VCF for new interpretation tool
- bring MAX_ALIGN_LENGTH and MAPPING_QUALITIES annotations from CPX variants to re-interpreted simple variants
- add new CLI argument and filter assembly based variants based on annotation MAPPING_QUALITIES, MAX_ALIGN_LENGTH
- filter out variants of size < 50
- Bug fix for the extreme edge case where after alignments de-overlapping, an alignment block is only 1 base long (#4962)
- Turn back on checking variant info fields against header in SV vcf writing (turned off temporarily long time ago but slipped attention after implementation stablized) (#5084)
- Various improvements (#4996)