Quick Start

From PileLine

PipeLine input files

PileLine is capable to handle, filter and compare genomic position files (GP) including standard pileup, BED,GFF, or VCF files.

Basically, GP are tabular files where the two first columns contain chromosome name and position coordinate respectively. Additional optional fields are accepted in PileLine, see an example of GP input file below:

10     118829     optional1     optional2     optional3     ...    
10     121207     optional1     optional2     optional3     ...
10     121337     optional1     optional2     optional3     ...
10     121636     optional1     optional2     optional3     ...

PipeLine Guided example

1. Download GP example files (pileup format) to your working directory:

1. Experiment 1.

Control1Files.zip

Case1Files.zip

1. Experiment 2.

Control2Files.zip

Case2Files.zip

Each .zip file contains 2 pileup files:

• Whole pileup file (.pileup)
• Variants against reference genome pileup file (.variants.pileup).

2. You may compare Case1 vs Control1 at variant level using pileline-2smc functionality. Try this command line:

$ cd DOWNLOADED_FILES_DIRECTORY 
$ sh YOUR_PATH_TO_PILELINE/cmd/pileline-2smc.sh 
–a ./Control1.pileup –b ./Case1.pileup
–v ./Control1varfilter.pileup –w ./Case1.variants.pileup 
–o ./myoutput1.txt

Executing this code you will obtain 3 output files:

• FileNAME1: Variants found in Case1 but not in Control1 (i.e. somatic point mutations or SNPs)
• FileNAME2: Variants found in Control1 but not in Case1 (i.e. somatic point mutations or SNPs)
• FileNAME3: Variants found in Case1 and in Control1 (i.e. germinal mutations or SNPs)

Now, run pileline-2smc to compare Case2 vs Control2:

$ sh YOUR_PATH_TO_PILELINE/cmd/pileline-2smc.sh 
–a ./Control2.pileup –b ./Case2.pileup
–v ./Control2.variants.pileup –w ./Case2.variants.pileup 
–o ./myoutput2.txt

3. You can also compare several samples at variant level:

$ sh YOUR_PATH_TO_PILELINE/cmd/pileline-nsmc.sh 
-a  -a 
-b  -b
-o 

4. At this point it could be useful to annotate SNPs in variants found between Case1 and Control1 to discard SNPs. To this end, you should execute pileline-fastjoin command as follows:

$ sh YOUR_PATH_TO_PILELINE/cmd/pileline-fastjoin.sh 
–a ./myoutput1.txt 
-b YOUR_PATH_TO_PILELINE/dbSNP130.txt --left-outer-join > ./mydbSNPannotation1.txt