Are there a heterozygous deletion?

[goldpm1]

Hi.

I have a small question.

Does filtered_large_svcalls.bedpe include heterozygous deletion?

On my result, NUM_READ_PAIR=0 was noticed in nearly all deletion calls, and Loupe Browser shows homozygous deletion.

Does single allele deletion is detectable in this filtered_large_svcalls.bedpe' or should I find these on large_cnv.bedpe ??

Thank you.

[fangli80]

Hello,
The filtered_large_svcalls.bedpe file include heterozygous deletions if detected. The SV calls in the large_cnv.bedpe file is detected from depth-based methods and are independent of filtered_large_svcalls.bedpe.
It's strange that NUM_READ_PAIR=0. Are you doing SV calling in a repeat region?