WES covarage analysis

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Surdan Burasi

• February 16, 2020 21:09

 

Can I do coverage analysis using gatk? the coverage I mentioned was 10x, 20x, 50x

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  SkyWarrior

  • February 17, 2020 09:24

  You can use CollectHsMetrics tool from gatk to perform coverage analysis of WES analyses. 

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  Surdan Burasi

  • February 18, 2020 07:41

  Hello dear SkyWarrior;

   

  What is the difference between BAIT_INTERVALS and TARGET_INTERVALS? 

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  SkyWarrior

  • February 18, 2020 08:05

  Bait intervals is a seperate file for indicating positions of your baits to capture target regions. Target intervals is the final bed file for the exome set. Some manufacturers serve bait intervals as a seperate file some do not. If you don't have it just use the same interval file for targets for both options. You will eventually pay attention to your target coverage and unique read mapping. 

   

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  Surdan Burasi

  • February 18, 2020 11:16

  thank you SkyWarrior :)

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