# SURVIVOR
Toolset for SV detection for short reads

**************************************

INSTALL:

Download SURVIVOR:
```
git clone https://github.com/fritzsedlazeck/SURVIVOR.git
```

  cd SURVIVOR/Debug
  
  make

**************************************

USAGE:
```
./SURVIVOR ID
```
to see the individual parameters for each option.

choose the ID from these options:
```
  1: Simulate  SV on genome
  2: Simulate PacBio reads
  3: Evaluate SV calling
  4: Merge SV calls (vcf) 
  5: Consensus call from 2/3 callers
  6: Extract genes influenced by SVs
  7: Filter and convert SV calls from Delly
  8: Filter and convert SV calls from Lumpy
  9: Filter and convert SV calls from Pindel
  10: Summarize MQ 0 coverage to bed file
```

**************************************
CONTACT:

If you have questions or encounter a problem please contact:
fritz.sedlazeck@gmail.com

# SURVIVOR
Toolset for SV detection for short reads

**************************************

INSTALL:

Download SURVIVOR:
```
git clone https://github.com/fritzsedlazeck/SURVIVOR.git
```

  cd SURVIVOR/Debug
  
  make

**************************************

USAGE:
```
./SURVIVOR ID
```
to see the individual parameters for each option.

choose the ID from these options:
```
1: Simulate SV on genome
2: Simulate PacBio reads
3: Evaluate SV calling
4: Merge SV calls (vcf) 
5: Consensus call from 2/3 callers
6: Extract genes influenced by SVs
7: Filter and convert SV calls from Delly
8: Filter and convert SV calls from Lumpy
9: Filter and convert SV calls from Pindel
10: Convert SV calls from Assemblytics
11: Summarize MQ 0 coverage to bed file
12: Summarize SVs events in VCF file
```

**************************************
CONTACT:

If you have questions or encounter a problem please contact:
fritz.sedlazeck@gmail.com

Update in the number of functions included
Update in the number of functions included