User: braveen.joseph

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Posts by braveen.joseph

<prev • 7 results • page 1 of 1 • next >
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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 5 days 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 3 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 4 months ago by braveen.joseph20 • updated 3 months ago by Guy Reeves850
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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 5 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 5 months ago by braveen.joseph20 • updated 5 months ago by Jennifer Hillman Jackson22k
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Answer: A: Uploading data to galaxy via FTP
... Thanks a lot Jen for the prompt reply! ...
written 5 months ago by braveen.joseph20
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Uploading data to galaxy via FTP
... Hi I'm currently using galaxy to analyze some genome sequences. I have uploaded my fastq to FTP. But I'm unable to load (Uploaded data is not recognized in galaxy) the data to history (to start analysis) via choose FTP files, Please Help ...
galaxy written 5 months ago by braveen.joseph20

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