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fritzsedlazeck / SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
MIT License
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Segmentation fault while annotating with a gff #9

Open madeleinesentucq opened 5 years ago

madeleinesentucq commented 5 years ago

Good afternoon,

I am trying to annotate and compare 2 SV callsets (2 identical mice : 1 with a disease and the other healthy). I have merged the two vcf files with survivor and and I wanted to annotate the resulting file with a gff file. Nevertheless I encountered a segmentation fault and I don't know how to resolve it.

This is what I get : 

$ ../../scripts/SURVIVOR_ant/bin/survivor_ant-core-0.1.0/survivor_ant -i sample_merged.vcf -g ../Mus_musculus.GRCm38.96_cleaned.gff3 
INITIALIZE VCF: 
Parse VCF: 0
Parse BED: 0
Parse GFF: 1
PRint: 
start printing
print entries 
Segmentation fault

If you have any idea on how to improve please let me know, Thank you for your time,

Madeleine