Identification of break points for a balanced translocation

Question

[nkausthu]

Hi,

From the karyotype results we could see a balanced translocation in one of the sample and we have whole genome data available for the same sample. It would be really great if someone can give suggestion in this regard. We have extracted the clipped reads aligned to both the chromosome and part of the reads which are clipped have been realigned to reference genome. We would like to cluster the reads which aligned to specific region. Any tools are available to perform this?

Answer 1

[trausch]

If you have paired-end whole genome data you can use Delly.

[nkausthu]

Thank you and I ran Delly for the paired end data. But its taking too much of time to give the results. As I have the karyotype results can I specify the specific chromosomes and run Delly?

[trausch]

You can just extract the 2 translocated chromosomes of interest:

samtools view -b <input.bam> chrA chrB > subset.bam
samtools index subset.bam

Or if you know the approximate regions:

samtools view -b <input.bam> chrA:10000000-20000000 chrB:50000000-60000000 > subset.bam
samtools index subset.bam

Answer 2

[Pierre Lindenbaum]

last year, I found a balanced translocation just by looking at the discordant pairs Identifying discordantly mapped reads .

There was a large number of pairs that were obviously clustered in the same region

a possible translocation ? pic.twitter.com/NH3BjkGof8

— Pierre Lindenbaum (@yokofakun) December 13, 2017