Low coverage WGS

[Felipe Luz Torres Silva]

Hi everyone.
I aim to identify translocations with ultra-low pass whole genome sequencing (~0,5X).

Im testing DELLY against some public data and DELLY didnt find the same translocations mentioned on papers (wich mention default parameters).

Is there any special data tratment dus to its low coverage?

I'm could see split reads on IGV proving the translocation EWSR1-FLI, but DELLY didn't call it.

How to proceed?
Thanks in advance

My pipleine: FASTQ >Quality check > BWA-MEM (-M paramenter) > DELLY (default)

All of it was done on Galaxy.

[Tobias Rausch]

I am not familiar with the Galaxy implementation. To increase sensitivity, you can set the mapping quality thresholds to 0 and lower the min. clipping length, e.g.: delly call -q 0 -r 0 -s 5 -c 5 ...

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