Interchromosomal translocations

[rahulk87]

Hi @walaj ,

I successfully ran svaba and annotated the output with your instructions. Just a quick question, is svaba detect only intrachromosomal translocations? In all my samples I just found only intrachromosomal trans and no interchromosomal.

Thanks, Rahul

[walaj]

Hi Rahul,

SvABA will detect both. Inter-chromosomal translocations comprise 20% of somatic rearrangements overall (although very very few germline rearrangements). Could be that there aren't any?

On Mon, Mar 18, 2019 at 2:57 PM Rahul Kumar [email protected] wrote:

Hi @walaj https://github.com/walaj ,

I successfully ran svaba and annotated the output with your instructions. Just a quick question, is svaba detect only intrachromosomal translocations? In all my samples I just found only intrachromosomal trans and no interchromosomal.

Thanks, Rahul

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[rahulk87]

I am analysing wgs data of 21 cell lines, I don't think so none of them have any inter-chromosomal translocation. Moreover I ran Manta and observed inter-cchr translocations. Is there any specific parameter I am missing to get inter-chr translocation or its by default?

My command: svaba run -t ${inbam} -p 8 -L 6 -I -a ${name} -G ${REF}

[rahulk87]

Just to add, one of my cell line is common with CCLE database and they reported inter-chromosomal translocation using svaba itself. It means, I am missing something in my command line run.

[rahulk87]

I think its because I used "-I" in my command line which is suppressing the inter-chr lookup, I am trying without "-I" now.

[rahulk87]

Now, I have the inter-chr translocations after removing the "-I" from the command line.

I have another question, I observed that in all the inter-chr translocations, number of spanning reads always "-1" and not actual number of reads, what does that mean?