User: braveen.joseph

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Posts by braveen.joseph

<prev • 12 results • page 1 of 2 • next >
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True variant not called by Varscan
... Hi, I'm using the Varscan tool to call SNPs and INDELs. There are some TRUE variants that are not called by this variant caller. I can clearly see them with IGV. For example there are 34 reads at a loci with all being mutant reads (100%), and still not called as a variant. I used a minimum read dep ...
galaxy varscan written 9 weeks ago by braveen.joseph20 • updated 9 weeks ago by Jennifer Hillman Jackson23k
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Answer: A: Add Unified Genotyper to Local instance
... Thanks a lot for the reply! ...
written 11 weeks ago by braveen.joseph20
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Add Unified Genotyper to Local instance
... HI There, I tried to install the tool Unified Genotyper from the tool shed, and I was unable to do it. Details follows, Name: Unified Genotyper SNP and indel caller Type: Unrestricted Revision: 0 (2014-04-01) Owner : devteam So I tried to add this tool manually into the galaxy local instance. I ...
galaxy unified genotyper written 11 weeks ago by braveen.joseph20
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Upload file to Galaxy local instance
... Hi, I'm trying to upload large data files via FTP using FileZilla. I am able to connect and upload files to FileZilla. I did configure galaxy and it gives the option to upload files via FTP. But when choose upload via FTP in local instance the data is not showing up. Can someone help me to rectif ...
local galaxy galaxy written 6 months ago by braveen.joseph20 • updated 6 months ago by Jennifer Hillman Jackson23k
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Filter SAM questions
... Hi, I don't know whether these are appropriate questions. I tried a lot to understand this, couldn't find any answers that satisfied me. So would like to give a try. (1) What is the difference between Mapped and Unmapped Reads? (As defined by the tool) (2) Is it absolutely necessary to use filter ...
sam galaxy written 6 months ago by braveen.joseph20 • updated 6 months ago by Jennifer Hillman Jackson23k
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Filter Varscan VCF
... Hello, I have a VCF file obtained from the Varscan tool. I want to filter the variants based on "FREQ". I tried several VCF filter and select tools. None Seemed to be working. For some reason, the VCF filter tool is not working properly. After filtering I get the same number of variants. Can som ...
varscan vcf filter written 6 months ago by braveen.joseph20
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Comment: C: Filtering Variants using Snpsift filter and SnpEff
... Hi, Thanks a lot for the reply. I think what you said above is working. What i actually wanted is... let's say there are 30 reads for a nucleotide site in the WGS alignment. If a mutation is present on a site, I wanted only the sites where the mutation is present in all 30 reads in my output file ( ...
written 10 months ago by braveen.joseph20
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Filtering Variants using Snpsift filter and SnpEff
... Hi, I have a bunch of variants in .VCF file which I got through the unified genotyper tool. Now I want to filter only the "Homozygous" (100% alternate allele frequency) variants. But the Snpsift filter and SnpEff tools do not have any option to change what on basis the variants are annotated as "Ho ...
galaxy snp written 10 months ago by braveen.joseph20 • updated 10 months ago by Guy Reeves1.0k
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Error- SAM to BAM tool in Galaxy local instance
... Hello there, I'm trying to implement the SAM-TO-BAM version 1.1.4 tool in Galaxy local instance. I got the following error. Traceback (most recent call last): File "/Users/Salmo08/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) ...
sam-to-bam galaxy written 12 months ago by braveen.joseph20
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Unified Genotyper ERROR (Deprecated tool at Galaxy Main http://usegalaxy.org)
... Hi, I got the following error using running cloudmap workflow. This Error occurs when I Unified genotyper. Anyone knows why? Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch -Xmx15872m -Xms256m [Thu Dec 01 21:54:47 CST 2016] net.sf.picard.sam.CreateSequenceDictionary REFERENCE= ...
galaxy gatk usegalaxy.org unified-genotyper error written 12 months ago by braveen.joseph20 • updated 12 months ago by Jennifer Hillman Jackson23k

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