[svtoolkit-help] Regarding sample test in Genome Strip

[Mishra, P. <Pam...@bc...>]

Hi,

I am trying to find SV for 100 samples of  chromosome 20.  I already ran preprocessing and discovery on these samples without any error. The problem is when I look at the final vcf file, I see only 2 samples being called out having SVs in the discovery phase. I checked the logs and it looks like its reading and also making stats for all the 100 files.

When I split the 100 samples in batches of 50 each (2 batches),one batch gives me the same 2 samples that show up in the 100 sample list. The  other batch gives me only 1 sample. This same sample does not show any SV when its included in the 100 samples. I have done such kind of tests several times but I always find the same pattern again and again.  I am not sure why this is happening. I understand there are a few filters listed here.(http://sourceforge.net/p/svtoolkit/mailman/message/28046131/)  But my idea was that the samples that show discordant pairs should show up both in the list of 100 as well as when I run only 50. Could you please throw your suggestion and insight into this situation. Is there checks to be done?

Any suggestion would be highly appreciated.

Thanks,
Pamela Mishra