Giuseppe1995

Is it possible to infer duplications/deletions/translocations/insertions/inversions from SvABA output?

2

Hi, I have a series of SvABA vcfs, and I wanted to know if it was possible to tell somehow the type of a variant, since the field "TYPE" has...

why my VCF file generated with manta is missing genotype information

4

Hi, everybody, I am pretty new to coding and bioinformatics. I am using Manta as a tool to infer somatic structural variants (SVs) from a paired tumor/normal sample call. However,...

Error while running smoove call: panic: sam: reference already used

5

Hi, I am trying to run `smoove call` on a set of matched normal-tumor bam files. I've properly run it on more than 100 WGS samples belonging to a dataset,...

Hi! I am trying to convert a Manta-called VCF structural variants file to bedpe format. here the code I use `svtools vcftobedpe -i somaticSV.vcf -o myFile.bedpe` and there the error...

Hi! I am trying to run cuffdiff on a previously merged gtf file i created with cuffmerge. The command I'm running is the following: `cuffdiff ./diff_exp -p 15 -b /srv/ngs/analysis/dalteriog/reference_genomes/hs/GRCh37.fa...

error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

5

### Checklist - [X] I added a descriptive title - [X] I searched for other issues and couldn't find a solution or duplication - [X] I already searched in Google...

Can not proceed without the required Python libraries, please install them and re-run

4

Hi! I am trying to install HiC-Pro 3.1.0 following the instructions on its github page [github page](https://github.com/nservant/HiC-Pro). When I try to configure HiC-Pro by typing ` make configure` in HiC-Pro-master...

Bug in `fviz_nbclust` function

2

Hi, I was trying to run `fviz_nbclust` function on a NbClust-derived list (actually, I was following this tutorial) which returned this error: > Error in if (class(best_nc) == "numeric") print(best_nc)...