Forum: Vendor Forum
06-19-2017, 06:35 PM
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Replies: 2
Views: 5,005
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.8.2. The changes in this version are listed below....
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Forum: Vendor Forum
06-01-2017, 06:59 PM
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Replies: 2
Views: 5,005
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.8.1. The changes in this version are listed below. ...
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Forum: Vendor Forum
05-15-2017, 08:38 PM
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Replies: 2
Views: 5,005
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Forum: Vendor Forum
10-17-2016, 03:08 PM
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Replies: 1
Views: 3,481
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.7.1. The changes in this version are listed below. ...
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Forum: Vendor Forum
08-25-2016, 08:28 PM
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Replies: 1
Views: 3,481
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Forum: Vendor Forum
03-13-2016, 06:06 PM
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Replies: 2
Views: 2,446
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.6.1. The changes in this version are listed below....
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Forum: Vendor Forum
01-25-2016, 11:05 AM
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Replies: 2
Views: 2,446
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.6.1. The changes in this version are listed below. ...
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Forum: Vendor Forum
12-06-2015, 06:50 PM
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Replies: 2
Views: 2,446
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Forum: Bioinformatics
10-18-2015, 03:36 PM
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Replies: 4
Views: 2,702
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Forum: Bioinformatics
10-18-2015, 12:54 PM
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Replies: 4
Views: 2,702
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Forum: Vendor Forum
10-15-2015, 05:33 PM
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Replies: 2
Views: 2,518
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.5.2. The changes in this version are listed below. ...
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Forum: Bioinformatics
10-04-2015, 02:53 PM
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Replies: 3
Views: 3,858
While this post is a little old, it is worth...
While this post is a little old, it is worth noting that the joint Bayesian variant calling of RTG Core (http://realtimegenomics.com/products/rtg-core/) does directly incorporate pedigree information...
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Forum: Bioinformatics
10-04-2015, 02:43 PM
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Replies: 1
Views: 2,458
If you are interested in the algorithms behind...
If you are interested in the algorithms behind indel calling in general, the method used by RTG Core (http://realtimegenomics.com/products/rtg-core/) for indel calling (and complex haplotype calling)...
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Forum: Illumina/Solexa
09-24-2015, 07:16 PM
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Replies: 3
Views: 1,336
"1" represents a haploid call, such as on the...
"1" represents a haploid call, such as on the non-PAR regions of X and Y for a male sample. RTG Core (http://realtimegenomics.com/products/rtg-core/) variant callers also automatically output haploid...
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Forum: Vendor Forum
09-07-2015, 02:53 PM
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Replies: 2
Views: 2,518
New stable releases are now available which...
New stable releases are now available which include minor improvements and bug fixes.
The first of these is our full analysis suite, RTG Core 3.5.1. The changes in this version are listed below. ...
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Forum: Vendor Forum
07-16-2015, 01:39 PM
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Replies: 2
Views: 2,518
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Forum: Bioinformatics
06-08-2015, 01:23 PM
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Replies: 5
Views: 7,323
Just noticing your comment about problem with...
Just noticing your comment about problem with indels when using MuTect. You might want to try the RTG somatic caller (part of RTG Core), which uses the same haplotype calling engine as the regular...
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Forum: Bioinformatics
05-28-2015, 01:52 PM
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Replies: 4
Views: 2,535
You should absolutely be using rtg vcfeval to...
You should absolutely be using rtg vcfeval to perform the comparison, as it correctly handles the differences in variant representation that different callers produce. Other comparison tools do not...
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Forum: Vendor Forum
05-27-2015, 02:23 PM
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Replies: 4
Views: 3,082
RTG Core 3.4.5 / RTG Tools 3.4.5
New stable releases are now available which include minor improvements and bug fixes. In particular, those using the somatic caller or vcfeval/rocplot will benefit from updating to the new release. ...
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Forum: Bioinformatics
05-13-2015, 12:52 PM
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Replies: 16
Views: 3,337
Jo,
The 1-50bp note is more about the...
Jo,
The 1-50bp note is more about the default RTG mapping settings (you'd have to start adjusting the aligner settings to look for longer indels, at somewhat of a speed penalty). The variant...
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Forum: Bioinformatics
05-11-2015, 03:59 PM
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Replies: 679
Views: 217,525
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Forum: Bioinformatics
05-11-2015, 02:46 PM
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Replies: 679
Views: 217,525
Hi Brian,
Could you please clarify the...
Hi Brian,
Could you please clarify the license for BBMap? I thought I might try a couple of runs with it for fun, but once I installed it I saw conflicting license information. In the top level of...
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Forum: Bioinformatics
05-03-2015, 01:18 PM
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Replies: 16
Views: 3,337
Hi Jo,
You can try the caller from RTG Core,...
Hi Jo,
You can try the caller from RTG Core, which will call the haplotypes over the region as a whole, and includes an allelic depth attribute in the VCF which should include exactly the counts...
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Forum: Vendor Forum
04-20-2015, 02:03 PM
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Replies: 4
Views: 3,082
RTG Core 3.4.4 / RTG Tools 3.4.4
New stable releases are now available which include minor improvements and bug fixes. In particular, heavy users of vcfeval or rocplot will benefit from updating to the new release.
The first of...
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Forum: Metagenomics
03-22-2015, 01:25 PM
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Replies: 7
Views: 2,443
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