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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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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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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…
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Hello @mjafin ,
We are testing vardict using our proxy bam file for somatic indel detection and are noticing several cases where very low evidence in the proxy bam (3-4 reads at an allele frequency o…
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I have seen the following exit message on error:
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
at java.lang.String.charAt(String.java:658)
at com…
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Hi,
I am trying to create an index for drop seq experiments using STAR. To fine tune our drop seq setup we need to have a mixture of human and mouse cell lines. Drop seq provides a meta fasta and gtf …
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This produces an error (used -k 0 to turn off local realignment):
VarDict -G human_g1k_v37_decoy.fasta -f 0.01 -h -b 'tumor.k.bam|normal.k.bam' -k 0 -Q 1 -c 1 -S 2 -E 3 -g 4 1.k.bed
The error message…
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We've been testing VarDictJava on whole genome analyses chunked into analyzable sections. We typically break up the genome at natural breakpoints without coverage to avoid accidentally splitting an an…