Red

Exception in thread "main" java.lang.IllegalStateException: Unable to delete: abra_temp_dir at abra.ReAligner.init(ReAligner.java:1102) at abra.ReAligner.reAlign(ReAligner.java:121) at abra.ReAligner.run(ReAligner.java:1240) at abra.Abra.main(Abra.java:12) please help me!!!

Hello, nh13, I have some question： 1. I wonder if the mutations in the vcf file in the output of DWGSIM are randomly generated and how to control the counts...

Disagreement between Intervene and BEDtools

4

Hello, Thank you for providing such a convenient tool! I have installed Intervene via conda and tested with my own dataset `hap1.bed` and `hap2.bed` to generate a Venn diagram using...

GermlineCNVCaller - python exited with 2

1

Hello, I'm testing gatk4.3 against 3 WES samples. For less time comsuption, I scattered the bed file into 45 small interval list. But an error prompted out in the GermlineCNVCaller...

python exited with 1. Theano error.

1

## Bug Report ### Affected tool(s) or class(es) GATK-gCNV-GermlineCaller ### Affected version(s) 4.3.0.0 ### Description ` 00:16:50.019 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/hpc/home/lijc/xiangxud/software/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 00:16:50.035 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so...

A lot of overlapping SV presented in delly's output

2

Hello, Recently I am using DELLY on a batch of WGS data (~30X) from 1000 Genome Project with the command `dellt call`, but there were many overlapping SV either the...