Martaprf

Error in using getBamCounts

1

Hi, I am trying to get the counts in my data but when I run getBamCounts I have the followed error: Error in countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges...

Lumpyexpress does not run but do not appears error messages, why it can happen?

10

Hi! I am trying run lumpy express with the follow command: /home/mferreira/programs/lumpy-sv/bin/lumpyexpress -v \ -B sample.bam \ -S sample.splitters.sorted.bam \ -D sample.discordants.sorted.bam \ -o sample.vcf and I don´t get any...

Error during installation

1

I am trying to install and I am using the following commands : `apt -y install autoconf intltool automake meson libsystemd-dev pkg-config ninja-build git libdbus-1-dev libinih-dev build-essential libgtk-3-dev libgtk-3-0 git...

Smoove docker cannot access files!

7

I am runing the docker like this: ``` docker run --cpus=20 --memory=25g --memory-swap=30g \ -v "/home/mferreira":"/input" \ -v "/home/mferreira":"/output" \ brentp/smoove smoove call -x \ --name /output/all.samples.lumpy --outdir /output/teste_smoove/ \...