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I got an exception while executing karkinos with following command.
```shell
java -Xmx15g -XX:+UseSerialGC -jar karkinos-standalone-2.0.4-SNAPSHOT.jar mergeresult -a /PATH/TO/ID.hg38_multianno.csv…
alumi updated
7 years ago
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In order to begin production of for the pharmacogenomics app as well as the discovery app we need to run a local instance of a mongoDB that can store annotated variant information in a queryable manne…
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Will be nice to have filters with > or < when annotations are numbers, I'm using ExAC and only with = and is not enough.
*EDIT*
I see that there are filters that allow you to use < and > but th…
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I was wondering if there are any plans to support GRCh38 as an additional assembly. The alternate loci and decoy sequences are likely to improve both variant calling and expression studies. I suppose …
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For now, I have just removed Intervar's check for the file and subsequent call to Annovar's Perl script. Perhaps you or I could review this section of Intervar code at some point.
```
Notice: Your c…
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NOTICE: Multianno output file is written to annotated/project.avinput.hg19_multianno.txt
PROGRESS: Extracting individual IDs
PROGRESS: Starting PSAP annotation
[1] "/pine/scr/m/a/martyf/project_fil…
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I am getting the following notices when trying to run the tool:
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_ALL.sites.2015_08.txt.gz ... Failed
…
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Have any hint on how to annotate the vardict results using annovar or snpeff?
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Some deletion variants which were previously identified manually from IonTorrent output may not have been included in reportIT pipeline output; need to verify whether or not this is the case, and if s…
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I really appreciate your work and thanks for your share.
And I also see annovar has intervar_20170202 database, but it only
has clinical interpretation of missense variants. I wonder why insert/de…