Hello Guys.
I'd running Lumpy on galaxy platform in order to find translocations.
But i intent to use ultra low coverage WGS data (~0,5 X).
I'd like to know with there are any parameter to set due to low coverage.
Also.. How can i pick a BND call and assume it is correct? I mean.. what is the best filter among all those present on vcf that can support this call? SU is a got parameter (with what threshold?), even if the BND is not PRECISE?
my pipeline:
BWA-MEM > Lumpy preprocessing > LUMPY
Hello Guys. I'd running Lumpy on galaxy platform in order to find translocations. But i intent to use ultra low coverage WGS data (~0,5 X).
I'd like to know with there are any parameter to set due to low coverage. Also.. How can i pick a BND call and assume it is correct? I mean.. what is the best filter among all those present on vcf that can support this call? SU is a got parameter (with what threshold?), even if the BND is not PRECISE?
my pipeline: BWA-MEM > Lumpy preprocessing > LUMPY
Sorry for many questions. Thanks in advance