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RTG Investigator 2.4
------------------------------
Major features of this release:
* mapx now has support for variable length and reads longer than
189nt. Bear in mind that as mapx currently performs global
alignment, longer reads will be less likely to have a high scoring
match - you may need to adjust alignment thresholds appropriately.
* The snp module for calling SNPs, MNPs, and indels now supports
haploid calling, and is faster (almost 2x faster for Complete
Genomics data).
* End to end handling of sex chromosomes in human variant
calling. After creating a one-off chromosome specification file for
your reference genome, mapping and variant calling commands allow
you to specify the sex of each individual being processed.
* Improved SNP calling accuracy for Ion Torrent.
* New somatic variant caller (commercial licensees only). As with the
singleton variant caller, this module is also able to utilize the
chromosome specification file to automatically produce appropriate
haploid/diploid calling on sex chromosomes.
* New pedigree-aware family variant caller (commercial licensees
only). This caller performs joint calling of all members of a family
(mother, father, and any number of sons/daughters). This
particularly improves the accuracy of variant calling when coverage
of each individual is low. As with the singleton caller, this module
is also able to utilize the chromosome specification file to
automatically produce appropriate haploid/diploid calls on sex
chromosomes.
Changes by command:
* family/somatic: These modules now implement complex calling and have
had many other improvements.
* family: Now produces a QUAL score.
* mapx: Much improved handling of variable length read sets -
previously read sets with more than a few nt deviation in length
were not supported (if attempted, mapping performance would degrade
with shorter reads). Variable length reads is now fully supported.
* mapx: Initial support for reads longer than 189nt.
* mapx: Handling of the --max-alignment-score for percentage based
thresholds was incorrect in that it was calculated based on the
pre-translated read length. This is now fixed and the flag
description has been updated.
* snp: Improvements to Ion Torrent snp calling (as determined by the
read group platform field being set to IONTORRENT).
* snp: Added new flag --ploidy to allow specifying whether to perform
haploid or diploid variant calling.
* snp: Switched to new internal architecture to more readily allow
multithreading. It no longer has a limit on the number of input SAM
files, however now the input SAM files must be tabixed (or indexed
BAM).
* snp: Fixed the handling of calling near boundaries of user-specified
--region locations (previously mappings overlapping the region
border were not being supplied to the snp caller).
* snp: CG snp calling speed is approximately 2x faster.
* map/snp/somatic/family: Added support for sex specific mapping and
variant calling by defining a reference configuration file and using
the appropriate --sex flag during mapping and snp calling. See the
user manual for more details.
* sdfstats: New option --sex to list the reference sequences along
with their ploidy for each sex.
* map/snp/somatic/family: Improvements have been made to the
calibration files produced during mapping allow snp calling coverage
filters to handle coverage variations per sequence (e.g. due to
varying ploidy on sex chromosomes). You can generate new calibration
files for existing mappings with the calibrate module.
* snp: New VCF filter RCEQUIV denotes when a variant is equivalent to
a previous variant (these typically occur at either end of
homopolymer regions).
* snp: New output file regions.bed.gz containing extra information
regarding the calling. Currently it lists the regions that were
called using complex calling.
* snp: QUAL scores for extremely confident calls were being capped at
1000000, however this was also including all scores above about
3000. QUAL scores are now more accurately output in the VCF.
* The .bz2 decompression library could not handle multi-member
files. This has been extended to support these files.
* extract: Bug fix when extracting vcf/coverage from a file containing
a single reference and no region was specified.
* extract: Bug fix for when the specified region contained an invalid
range.
* all: Updated the bundled JVM to 1.6.0_29
* windows: Fixed a problem when RTG was installed to a location
containing spaces in the path name.
------------------------------
Major features of this release:
* mapx now has support for variable length and reads longer than
189nt. Bear in mind that as mapx currently performs global
alignment, longer reads will be less likely to have a high scoring
match - you may need to adjust alignment thresholds appropriately.
* The snp module for calling SNPs, MNPs, and indels now supports
haploid calling, and is faster (almost 2x faster for Complete
Genomics data).
* End to end handling of sex chromosomes in human variant
calling. After creating a one-off chromosome specification file for
your reference genome, mapping and variant calling commands allow
you to specify the sex of each individual being processed.
* Improved SNP calling accuracy for Ion Torrent.
* New somatic variant caller (commercial licensees only). As with the
singleton variant caller, this module is also able to utilize the
chromosome specification file to automatically produce appropriate
haploid/diploid calling on sex chromosomes.
* New pedigree-aware family variant caller (commercial licensees
only). This caller performs joint calling of all members of a family
(mother, father, and any number of sons/daughters). This
particularly improves the accuracy of variant calling when coverage
of each individual is low. As with the singleton caller, this module
is also able to utilize the chromosome specification file to
automatically produce appropriate haploid/diploid calls on sex
chromosomes.
Changes by command:
* family/somatic: These modules now implement complex calling and have
had many other improvements.
* family: Now produces a QUAL score.
* mapx: Much improved handling of variable length read sets -
previously read sets with more than a few nt deviation in length
were not supported (if attempted, mapping performance would degrade
with shorter reads). Variable length reads is now fully supported.
* mapx: Initial support for reads longer than 189nt.
* mapx: Handling of the --max-alignment-score for percentage based
thresholds was incorrect in that it was calculated based on the
pre-translated read length. This is now fixed and the flag
description has been updated.
* snp: Improvements to Ion Torrent snp calling (as determined by the
read group platform field being set to IONTORRENT).
* snp: Added new flag --ploidy to allow specifying whether to perform
haploid or diploid variant calling.
* snp: Switched to new internal architecture to more readily allow
multithreading. It no longer has a limit on the number of input SAM
files, however now the input SAM files must be tabixed (or indexed
BAM).
* snp: Fixed the handling of calling near boundaries of user-specified
--region locations (previously mappings overlapping the region
border were not being supplied to the snp caller).
* snp: CG snp calling speed is approximately 2x faster.
* map/snp/somatic/family: Added support for sex specific mapping and
variant calling by defining a reference configuration file and using
the appropriate --sex flag during mapping and snp calling. See the
user manual for more details.
* sdfstats: New option --sex to list the reference sequences along
with their ploidy for each sex.
* map/snp/somatic/family: Improvements have been made to the
calibration files produced during mapping allow snp calling coverage
filters to handle coverage variations per sequence (e.g. due to
varying ploidy on sex chromosomes). You can generate new calibration
files for existing mappings with the calibrate module.
* snp: New VCF filter RCEQUIV denotes when a variant is equivalent to
a previous variant (these typically occur at either end of
homopolymer regions).
* snp: New output file regions.bed.gz containing extra information
regarding the calling. Currently it lists the regions that were
called using complex calling.
* snp: QUAL scores for extremely confident calls were being capped at
1000000, however this was also including all scores above about
3000. QUAL scores are now more accurately output in the VCF.
* The .bz2 decompression library could not handle multi-member
files. This has been extended to support these files.
* extract: Bug fix when extracting vcf/coverage from a file containing
a single reference and no region was specified.
* extract: Bug fix for when the specified region contained an invalid
range.
* all: Updated the bundled JVM to 1.6.0_29
* windows: Fixed a problem when RTG was installed to a location
containing spaces in the path name.