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I downloaded and successfully used the binaries from https://github.com/lomereiter/sambamba/releases. However, I'm failing to compile the source code under CentOS machine. The machine was missing `ldm…
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Hello,
I have been running the Perl version of varDict before I realized I can switch to the Java version. Running nearly identical commands:
`./build/install/VarDict/bin/VarDict -G ucsc.hg19.fasta …
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Template command on the yaml file with qsignature duplicates the entry in the alignment section and the top level of the sample yaml
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I've turned off massive contraction, setting the boolean to False. The major motivation is that if one parameter has a too large influence, it needs to be contracted several times to get into balance …
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Hi
I am starting to use multiqc to summarise RNASeq analysis reports - it is amazingly useful.
I noticed though that the samtools "Reads Mapping" plot and mouseovers are slightly misleading as the c…
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AZ kindly contributed the simple_sv_annotation script, which is hosted by bioconda and used in bcbio. I have a minor bugfix for this module; however, it seems to be vanished from the AZ github reposit…
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Hi,
I have been running the process below for almost 3 days. It went without a problem until this step. I did not change anythin in the configuration related to mutation calling but I dont know why d…
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VarDictJava (and presumably VarDict) completely ignore reads that are missing the _optional_ `NM` tag, but this isn't clearly stated in any documentation, nor are any warnings issued while running. I…
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Dear @mjafin and @chapmanb;
I am getting the followed error. As I experienced a little bit from my previously asked issues, I realised that it might be related with Java version. Am I missing somethi…
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Hello,
I have been trying to apply the java version of your verdict program on a set of tumor/normal samples that have been modified according to GATK best practices for RNA (Recal, Realign, dedup, e…