ryanlayer
commented
6 years ago This is very strange. My expectation and experience is that more samples gives wider/longer VCFs. Can you send me the two commands? Is it possible that the 5-7 errors out due to memory issues?
On Thu, Apr 12, 2018 at 5:51 AM, CBorreda notifications@github.com wrote:
Hi Ryan!
I've been using Lumpy to detect SVs in plant genomes for a while. We were using them in 2-3 batches and it worked perfectly. Now I wanted to check SVs in a family so we run it for several samples on the same run. However, it failed to find some real SVs (by real I mean clearly visible when looking at IGV + PCR-confirmed) of a considerable size (few kb deletions and translocations). This problem arises only when using 5-7 samples; using 2 those SVs are detected. I thought that, by adding samples, the VCF would just get wider and longer, but I didn't expect it to actually substract samples. Is there something I'm missing here?
Thank you
Carles
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-- Ryan Layer
Hi Ryan!
I've been using Lumpy to detect SVs in plant genomes for a while. We were using them in 2-3 samples batches and it worked perfectly. Now I wanted to check SVs within a family so we run it for several samples on the same run. However, it failed to find some real SVs (by real I mean clearly visible when looking at IGV + PCR-confirmed) of a considerable size (few kb deletions and translocations). This problem arises only when using 5-7 samples; using 2 those SVs are detected. I thought that, by adding samples, the VCF would just get wider and longer, but I didn't expect it to actually substract variations. Is there something I'm missing here?
Thank you
Carles