Translocation Calling in human cancer given VCF and BAM files

Question

[jnf3769]

Hey Biostars,

I am a bit rusty on my genomics tools and was looking for a recommendation for calling translocations in human cancer. I have vcf and bam files (with indecies) that seem to be the result of a few calls to GATK (HaplotypeCaller, IndelRealigner, and BaseRecalibrator).

Any suggestions on what I should use, given these files (and access to references)? Bonus internet points if it is part of the larger GATK, but whatever works. I usually don't have an issue getting programs up and running.

Thank you kindly for your time and attention to this matter

Answer 1

[Kevin Blighe]

pindel can certainly attempt to detect these but it is switched off by default in order to save memory. Take a look at the following parameters that can be passed to the pindel command itself:

-k/--report_breakpoints
report breakpoints (default false)

-I/--report_interchromosomal_events
search for interchromosomal events. Note: will require the computer to have at least 4 GB of memory (default false) 

-b/--breakdancer
Pindel is able to use calls from other SV methods such as BreakDancer to further increase sensitivity and specificity. BreakDancer result or calls from any methods must in the format: ChrA LocA stringA ChrB LocB stringB other

Kevin