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WGLab / LinkedSV

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Are there a heterozygous deletion? #24

Open goldpm1 opened 3 years ago

goldpm1 commented 3 years ago

Hi.

I have a small question.

Does filtered_large_svcalls.bedpeinclude 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 commented 3 years ago

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?