Question: Translocation Calling in human cancer given VCF and BAM files
gravatar for jnf3769
10 months ago by
United States
jnf376940 wrote:

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

ADD COMMENTlink modified 10 months ago by Kevin Blighe42k • written 10 months ago by jnf376940
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe42k
Guy's Hospital, London
Kevin Blighe42k wrote:

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:

report breakpoints (default false)

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

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


ADD COMMENTlink written 10 months ago by Kevin Blighe42k
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