Translocations - CTX

[AriadnaColmeneroCobo]

I am just analyzing some structural variants in a de-duplicated BAM file. I have just noticed that following your code I can plot Deletions or Duplications. However, I have not seen the code to plot these CTX (although there's an example between chr 2/x in your paper). Could you please, indicate me how to change my code to add the mate chr and plot my translocation? Imagine I want to plot a translocation between chrX and chr2, how could I add the information about chr2 in this line of code?

time samplot plot -n sample_name -b /path/x.BAM -o X.png -c chrX -s 1000000 -e 2000000 -t CTX

Thank you so much and sorry for the inconvenience

[mchowdh200]

Various SV callers tend to label translocations differently. A lot of them simply label them as BND. Can you try using that as your -t arg?

[AriadnaColmeneroCobo]

I have already used this argument. However, I still do not know where to write the coordinates of the mate. In other words, considering a t(2;X), in my code there is only information about chr2. How should I write with the same line of code, the information about chrX to represent the translocation? Should I add another argument?

time samplot plot -n sample_name -b /path/x.BAM -o X.png -c chr2 -s 1000000 -e 2000000 -t BND

Thank you so much,

[mchowdh200]

Ah, I glossed over that part of your example. You can add a second set of -c/-s/-e for the other end of the translocation. For an example, see the usage in our functional tests. https://github.com/ryanlayer/samplot/blob/70cad157e7764c59a6149538305dcccaea8e11b9/test/func/samplot_test.sh#L448

[AriadnaColmeneroCobo]

Thank you so much!! When I plot it, there are a lot of paired reads, split reads, duplications,... in that zone. How could I assess which is my translocation?