aganezov / rck Goto Github PK

Hello,

I'm super excited to test this tool out. I'm currently testing it out with the LongRanger output and the 10X-specific TitanCNA workflow. I keep getting this error message when one of the SVs falls out side the telomeric regions/CNV regions.

Is there a parameter I can use to ignore these calls or do I have to filter my adjacencies input? Similarly, LongRanger calls a chromosomal deletions of chrY in females, is their a way to ignore these or do I need to filter them.

Thanks,
Melissa

telomere_positions=input_telomere_positions) File "/home/mzwaig/.local/lib/python3.7/site-packages/rck/core/structures.py", line 1590, in refined_scnt_with_adjacencies_and_telomeres "".format(positions=",".join(map(lambda p: p.stable_id_non_hap, bad_positions)))) ValueError: Either adjacency or telomere positions (8:-146370000) do not lie within segment