RTG Core 3.10 / RTG Tools 3.10
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RTG Announcements
Oct 29, 2018, 5:02:01 PM10/29/18
to RTG Announcements
Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core, and our utility package, RTG Tools. This release includes new features and bugfixes and Java compatibility improvements. Some of the highlights of this release:
* Several improvements to simulation tools. In particular, a new command pedsamplesim has been included that makes it very easy to simulate multiple samples at once, given a pedigree file. pedsamplesim automatically simulates founder individuals, inheritance by children, and de novo mutations.
* Java 11 compatibility testing. RTG is compatible with Java 11, although currently we recommend Java 8 for performance reasons. Also note that due to differences in Java Math library implementation after Java 8, in rare situations minor output differences may be observed when comparing results obtained using Java 8 with later Java versions. Builds that include a bundled JRE have been updated to the latest JRE 8u181.
Commercial users of RTG Core may download the update from our website at http://realtimegenomics.com/products/rtg-core-downloads. Non-commercial users can download the update from our website at http://realtimegenomics.com/products/rtg-core-non-commercial or build from the source on github at https://github.com/RealTimeGenomics/rtg-core.
Users of RTG Tools, which is made freely available for non-commercial or commercial use alike, can download the new version from our website at http://realtimegenomics.com/products/rtg-tools or build from the source code on github at https://github.com/RealTimeGenomics/rtg-tools.
Detailed changes are listed below by area. For more information on new features, see the RTG Operations Manual which is included within the distribution as HTML and PDF.
### Basic Formatting and Mapping
* petrim: Now outputs read length distribution statistics.
* petrim: Fixed an incorrect filename extension being used for fragment
and overlap length distribution output files.
* map: Now allows the use of both --repeat-freq and
--blacklist-threshold at the same time.
* map: Unmapped but placed reads have had minor adjustments made to
their expected mapping position. As well as causing changes to BAM
annotations, this can cause subsequent changes to variant calling
annotations (such as AVR scores).
* map: Fix a rare crash that could occur when mapping a male sample. The
fix for this can similarly have some changes to subsequent variant calling.
* sammerge: New flag --min-read-length to permit filtering out
alignments where the read length is below the specified threshold.
* sammerge: New flag --select-read-group to include only alignments from
the specified read groups.
* sammerge: New flag --remove-duplicates to detect and remove duplicate
reads based on mapping position. This is like the duplicate detection
that the analysis tools such as variant callers normally perform on
the fly.
* sammerge: Supports --Xforce to allow overwriting existing output
files.
* sdfsubset/sdfsplit: These commands now pass SAM read group information
from the input SDF to the output SDF.
### Variant Calling
* variant callers: The GT fields for unphased calls are now in a
normalized (numerically increasing) format. Previously the choice of
allele ordering for alleles within a GT field was somewhat arbitrary,
giving the impression of some significance where there was none.
* variant callers: Population variants loaded via --population-priors
are only used to refine complex call regions when the non-reference
allele fractions for the variant are higher than 1%. Previously the
use of a population priors source such as gnomAD that includes many
rare variants could lead to reduced sensitivity.
* variant callers: Improved the ability to identify candidate local
haplotypes when jointly calling a large number of samples or where
there is wide variation in coverage between samples. The effect of
this is greater sensitivity to rare variants such as singletons and de
novo variants.
* variant callers: Ignore SAM records where the reads have zero length.
* many: Region based SAM/BAM record retrieval could sometimes skip
records in the case of a small inter-region gap.
* segment: The --min-panel-coverage option has been renamed to
--min-norm-control-coverage (with extended functionality).
* avrbuild: New flag --annotated that allows supplying positive/negative
labels via annotations on each VCF record, as an alternative to
supplying separate positive and negative VCFs. The supported
annotation is the same as produced by vcfeval --output-mode=annotate
format.
* avrbuild: New flag --bed-regions to only read those training instances
that overlap the specified regions. This is a convenience method that
can be used to train on a specific subset of the data.
### Variant Processing and Analysis
* svdecompose: Fixed a crash caused by records where SVTYPE=INS but
where the record did not also contain an SVLEN annotation. These
records are now ignored.
* vcfdecompose: Fixed a crash on records that did not contain a GT
format field. This also affected vcfeval when using --decompose. In
addition, the error reporting for records with invalid GT fields has
been improved.
* many: Clearer error handling for VCF records that are invalid due to
extra TABs
* rocplot: Move the legend for precision/sensitivity graphs to the left
hand side, where it is less likely to obstruct the curves themselves.
* vcfannotate: Change in matching semantics when annotating with
IDs. Now uses the span of the record rather than just the start
position.
* many: New derived annotation VAF1 that contains the VAF of the most
frequent alt allele. Being a single value annotation, it can be easily
used during AVR model building.
* vcfmerge: Fix a crash that could occur when trying to merge a record
containing duplicated alleles.
### Other
* samplesim: Changed the behaviour when simulating from VCF records
without an AF annotation. Now these variants are ignored (i.e. never
selected for use by the sample), previously samplesim would treat all
alleles as equally likely. The old behaviour is available via new flag
--allow-missing-af.
* childsim: The misleadingly named flag --num-crossovers has been
renamed to --extra-crossovers.
* denovosim: Now allows the original and derived sample names to be the
same, in which case the sample in the output VCF is updated rather
than creating a new sample column.
* denovosim: No longer sets the DN flag to "N" for samples not receiving
the de novo mutation, as in multi-sample simulation scenarios this is
not a reliable indicator.
* denovosim: Fix bug when determining if a putative de novo site would
overlap with pre-existing variants.
* pedsamplesim: New command that allows simulating several samples in
one run according to a pedigree. This uses the methods of samplesim,
denovosim, and childsim to greatly ease the simulation of multiple
samples.
* pedstats: New flag --delimiter that can be used to output sample
identifiers with an alternative delimiter. For example, use comma as a
delimiter when directly supplying a sample list to vcfsubset
--keep-samples.
* simulation tools: Most commands now support --Xforce to overwrite
existing files.
* simulation tools: Improvements have been made to parameter validation.
* misc: Updates for compatibility with Java 11. However, for performance
reasons we recommend using Java 8 for computationally intensive
analysis such as mapping and variant calling.
* misc: Update bundled JRE to 1.8.0_181.
* misc: Improved percentage memory allocation behaviour when total
system memory can not be determined. Will now fall back to Java
default memory allocation.
* Several improvements to simulation tools. In particular, a new command pedsamplesim has been included that makes it very easy to simulate multiple samples at once, given a pedigree file. pedsamplesim automatically simulates founder individuals, inheritance by children, and de novo mutations.
* Java 11 compatibility testing. RTG is compatible with Java 11, although currently we recommend Java 8 for performance reasons. Also note that due to differences in Java Math library implementation after Java 8, in rare situations minor output differences may be observed when comparing results obtained using Java 8 with later Java versions. Builds that include a bundled JRE have been updated to the latest JRE 8u181.
Commercial users of RTG Core may download the update from our website at http://realtimegenomics.com/products/rtg-core-downloads. Non-commercial users can download the update from our website at http://realtimegenomics.com/products/rtg-core-non-commercial or build from the source on github at https://github.com/RealTimeGenomics/rtg-core.
Users of RTG Tools, which is made freely available for non-commercial or commercial use alike, can download the new version from our website at http://realtimegenomics.com/products/rtg-tools or build from the source code on github at https://github.com/RealTimeGenomics/rtg-tools.
Detailed changes are listed below by area. For more information on new features, see the RTG Operations Manual which is included within the distribution as HTML and PDF.
### Basic Formatting and Mapping
* petrim: Now outputs read length distribution statistics.
* petrim: Fixed an incorrect filename extension being used for fragment
and overlap length distribution output files.
* map: Now allows the use of both --repeat-freq and
--blacklist-threshold at the same time.
* map: Unmapped but placed reads have had minor adjustments made to
their expected mapping position. As well as causing changes to BAM
annotations, this can cause subsequent changes to variant calling
annotations (such as AVR scores).
* map: Fix a rare crash that could occur when mapping a male sample. The
fix for this can similarly have some changes to subsequent variant calling.
* sammerge: New flag --min-read-length to permit filtering out
alignments where the read length is below the specified threshold.
* sammerge: New flag --select-read-group to include only alignments from
the specified read groups.
* sammerge: New flag --remove-duplicates to detect and remove duplicate
reads based on mapping position. This is like the duplicate detection
that the analysis tools such as variant callers normally perform on
the fly.
* sammerge: Supports --Xforce to allow overwriting existing output
files.
* sdfsubset/sdfsplit: These commands now pass SAM read group information
from the input SDF to the output SDF.
### Variant Calling
* variant callers: The GT fields for unphased calls are now in a
normalized (numerically increasing) format. Previously the choice of
allele ordering for alleles within a GT field was somewhat arbitrary,
giving the impression of some significance where there was none.
* variant callers: Population variants loaded via --population-priors
are only used to refine complex call regions when the non-reference
allele fractions for the variant are higher than 1%. Previously the
use of a population priors source such as gnomAD that includes many
rare variants could lead to reduced sensitivity.
* variant callers: Improved the ability to identify candidate local
haplotypes when jointly calling a large number of samples or where
there is wide variation in coverage between samples. The effect of
this is greater sensitivity to rare variants such as singletons and de
novo variants.
* variant callers: Ignore SAM records where the reads have zero length.
* many: Region based SAM/BAM record retrieval could sometimes skip
records in the case of a small inter-region gap.
* segment: The --min-panel-coverage option has been renamed to
--min-norm-control-coverage (with extended functionality).
* avrbuild: New flag --annotated that allows supplying positive/negative
labels via annotations on each VCF record, as an alternative to
supplying separate positive and negative VCFs. The supported
annotation is the same as produced by vcfeval --output-mode=annotate
format.
* avrbuild: New flag --bed-regions to only read those training instances
that overlap the specified regions. This is a convenience method that
can be used to train on a specific subset of the data.
### Variant Processing and Analysis
* svdecompose: Fixed a crash caused by records where SVTYPE=INS but
where the record did not also contain an SVLEN annotation. These
records are now ignored.
* vcfdecompose: Fixed a crash on records that did not contain a GT
format field. This also affected vcfeval when using --decompose. In
addition, the error reporting for records with invalid GT fields has
been improved.
* many: Clearer error handling for VCF records that are invalid due to
extra TABs
* rocplot: Move the legend for precision/sensitivity graphs to the left
hand side, where it is less likely to obstruct the curves themselves.
* vcfannotate: Change in matching semantics when annotating with
IDs. Now uses the span of the record rather than just the start
position.
* many: New derived annotation VAF1 that contains the VAF of the most
frequent alt allele. Being a single value annotation, it can be easily
used during AVR model building.
* vcfmerge: Fix a crash that could occur when trying to merge a record
containing duplicated alleles.
### Other
* samplesim: Changed the behaviour when simulating from VCF records
without an AF annotation. Now these variants are ignored (i.e. never
selected for use by the sample), previously samplesim would treat all
alleles as equally likely. The old behaviour is available via new flag
--allow-missing-af.
* childsim: The misleadingly named flag --num-crossovers has been
renamed to --extra-crossovers.
* denovosim: Now allows the original and derived sample names to be the
same, in which case the sample in the output VCF is updated rather
than creating a new sample column.
* denovosim: No longer sets the DN flag to "N" for samples not receiving
the de novo mutation, as in multi-sample simulation scenarios this is
not a reliable indicator.
* denovosim: Fix bug when determining if a putative de novo site would
overlap with pre-existing variants.
* pedsamplesim: New command that allows simulating several samples in
one run according to a pedigree. This uses the methods of samplesim,
denovosim, and childsim to greatly ease the simulation of multiple
samples.
* pedstats: New flag --delimiter that can be used to output sample
identifiers with an alternative delimiter. For example, use comma as a
delimiter when directly supplying a sample list to vcfsubset
--keep-samples.
* simulation tools: Most commands now support --Xforce to overwrite
existing files.
* simulation tools: Improvements have been made to parameter validation.
* misc: Updates for compatibility with Java 11. However, for performance
reasons we recommend using Java 8 for computationally intensive
analysis such as mapping and variant calling.
* misc: Update bundled JRE to 1.8.0_181.
* misc: Improved percentage memory allocation behaviour when total
system memory can not be determined. Will now fall back to Java
default memory allocation.
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