search

nf-cmgg / structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
https://nf-cmgg.github.io/structural/
MIT License
18 stars 3 forks source link

Some bugs found the output of the pipeline #88

Open nvnieuwk opened 4 months ago

nvnieuwk commented 4 months ago

Description of the bug

  1. wisecondorx reports SVLEN wrong I guess: 
    chr21   13900001    wisecondorx_344 N   <DEL>   .   PASS    CNV_RATIO=-0.0368;ZSCORE=-8.95856;SVTYPE=CNV;END=24100000;SVLEN=1;CALLERS=wisecondorx   GT:CN   .:0
chr21   24100001    wisecondorx_345 N   <DUP>   .   PASS    CNV_RATIO=0.1254;ZSCORE=23.8602;SVTYPE=CNV;END=25700000;SVLEN=1;CALLERS=wisecondorx GT:CN   .:0
  2. not sure if this is a bug or not but in qdnaseq tool thereis only result for chr18,chrX and chrY
  3. SVLEN is missing in DELLY

Issues reported by @kubranarci, thank you!

Command used and terminal output

No response

Relevant files

No response

System information

No response

nvnieuwk commented 4 months ago

The first issue is a bug in bedgovcf which has been fixed in version 0.1.1. I'll update the version in the pipeline.