why the same genetic data could go both ways

ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.

http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html

GNU General Public License v3.0

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why the same genetic data could go both ways #284

Closed jielab closed 6 years ago

jielab commented 6 years ago

Hi, I am able to finally make DNG work on the example data. Once I run dng dnm auto --ped sample_CEU.ped --bcf sample_CEU.vcf, the output shows a total of 3 variants are de novo. Please see the screenshot below, the proband and the 3 variants highlighted in red.

My question is, the other variant not highlighted in red has the same genetic data as the last variant, except that the REF/ALT is different. Why this variant is not deeded de novo by DNG?

Best regards, Jie

capture

reedacartwright commented 6 years ago

Row 4 is a duplicate for row 3 and is probably being ignored by dng-dnm.

mpileup does unexpected things around indels, sometimes producing duplicated sites.