Body: <p>I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples. 
  I have been using SU/AC as one of my filters, looking for variants that have a minimum threshold of support per alternate allele called. Now I'm confused by some of the variants that are getting filtered out, and wonder why SU (number of pieces of evidence supporting the variant) is not calculated as I had expected.</p>
  
  <p>For one variant, if I sum the AS values (split-read observation counts) and the AP values (paired-end observation counts) over all 46 individuals, I get AS=24 and AP=15, so 39 total reads supporting the variant in the population. However, SU is only 14 (PE=5 + SR=9).</p>
  
  <p>Can anyone tell me why the values for SU, PE, SR are so much lower than the total AS &amp; AP counts? Thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-22T14:39:30.000Z
Comments.Text: We welcome this question here, but you may get a quicker and more thorough response posting to the [smoove issue tracker](https://github.com/brentp/smoove/issues).
Comments.UserDisplayName: Daniel Standage
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-01-25T18:08:13.050Z
Comments.Text: Thanks - it's now posted here: https://github.com/brentp/smoove/issues/53
Comments.UserDisplayName: Joanne
Tags: <vcf><structural-variation>
Title: structural variants: why doesn't AS + AP = SU?
ThreadText: # structural variants: why doesn't AS + AP = SU?
  
  (Asked by: username_0 on 2019-01-21)
  
  I have run smoove then duphold on 46 individuals, then pasted the duphold output back into a squared vcf with all 46 samples.
  I have been using SU/AC as one of my filters, looking for variants that have a minimum threshold of support per alternate allele called. Now I'm confused by some of the variants that are getting filtered out, and wonder why SU (number of pieces of evidence supporting the variant) is not calculated as I had expected.
  
  For one variant, if I sum the AS values (split-read observation counts) and the AP values (paired-end observation counts) over all 46 individuals, I get AS=24 and AP=15, so 39 total reads supporting the variant in the population. However, SU is only 14 (PE=5 + SR=9).
  
  Can anyone tell me why the values for SU, PE, SR are so much lower than the total AS & AP counts? Thank you!
  
  **Tags:** vcf, structural-variation
  
  > **Comments:**
  > **username_1**: We welcome this question here, but you may get a quicker and more thorough response posting to the [smoove issue tracker](https://github.com/brentp/smoove/issues).  
  > **username_0**: Thanks - it's now posted here: https://github.com/brentp/smoove/issues/53  
  
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  ## 0 answers
  
  