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Old 02-23-2016, 01:51 AM   #1
2nelly
Junior Member
 
Location: switzerland

Join Date: Feb 2016
Posts: 7
Default Indelocator and Breakdancer queries

Hello to everybody,

Since i am new in the field of bioinformatics, i have 2 questions regarding 2 different softwares.

1) Does anybody could propose me the correct command to run Indelocator. The documentation is very poor in CGA and Indelocator is not supported any more by GATK
I suppose it should be something like:
java -jar path/indelocator.jar -T ???? -R: path/reference.fasta -I:normal path/normal.bam -I:tumor path/tumor.bam -o path/output.vcf

2) Regarding Breakdancer, i notice that in all my configuration files the lower key is 0, which means that BreakDancerMax will detect insertions using read pairs that are at most 0 bp apart. That s why i suppose that i am always getting 0 insertions in my sample. I tried to manually change lower key from 0 to 100 and i got a lot of insertions in my output file, but i was wondering how accurate this output can be since i changed it manually. I guess 0!!!! I got tones of insertions....So,does anybody know why in my initial cfg file all lower key is always 0?

I would appreciate any suggestion...
thanks a lot!

Last edited by 2nelly; 02-23-2016 at 07:01 AM.
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