Question: Identification of break points for a balanced translocation
0
gravatar for nkausthu
8 months ago by
nkausthu20
nkausthu20 wrote:

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?

ADD COMMENTlink modified 8 months ago by Pierre Lindenbaum120k • written 8 months ago by nkausthu20
1
gravatar for trausch
8 months ago by
trausch1.2k
Germany
trausch1.2k wrote:

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

ADD COMMENTlink written 8 months ago by trausch1.2k

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?

ADD REPLYlink written 8 months ago by nkausthu20

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
ADD REPLYlink modified 8 months ago • written 8 months ago by trausch1.2k
0
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

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

ADD COMMENTlink written 8 months ago by Pierre Lindenbaum120k
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