This is a readme file for BasePlayer
Author: Riku Katainen @ University of Helsinki
Tumor Genomics Group (http://research.med.helsinki.fi/gsb/aaltonen/) 
Contact: riku.katainen@helsinki.fi
Visit https://baseplayer.fi for more information
See the BasePlayer manuscript at bioRxiv: https://doi.org/10.1101/126482
Instructional videos can be viewed at our Youtube channel https://www.youtube.com/channel/UCywq-T7W0YPzACyB4LT7Q3g 

Requires Java 7 (JRE 1.7) or newer.

Usage:
Click Launcher.jar to start BasePlayer.

Reserve more memory to BasePlayer by changing MemoryLimit=1200m -value in config_baseplayer.txt in your home directory to e.g. MemoryLimit=4G
Use Launcher.jar to apply change.
 
vcf and bed -files must be bgzipped and tabix-indexed (.vcf.gz and .vcf.gz.tbi
or .bed.gz .bed.gz.tbi).

Calculate amino acid changes for variants:
	open vcf-file
	Click Variant Manager -> Annotate

For optimal usage, you should have vcf and bam/cram -files for each sample. 
e.g. in case you have a sample named as sample1, name all files similarly and 
place in the same folder:
	
	sample1.vcf.gz
	sample1.vcf.gz.tbi
	sample1.bam
	sample1.bam.bai

	When you open sample1.vcf.gz, sample1.bam is recognized and opened 
	on the same track.

Enjoy!