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Some questions about the UG,BQSR,Indel realigner..

Hi !

I've got some question about some of the GATK tools and practices (and hope its okay to post them into a single thread)

  1. Is there any additional background information about the UnifiedGenotyper available , especially in case of multi sample calling ? How this works in a bit more detailed way ? So far I could only find the slides from the last GATK Workshop. But if I remember this correctly, during the presentation it was mentioned one could ask if more information is required (unfortunately I wasn't at the workshop ;))

  2. What's the definition of the Base Score Accuracy (Base Quality Score Recalibration Plots) ? Am I correct that this specifies how well the observed quality scores match the expected (empirical) quality scores ? I think I read it somewhere but couldn't find it any more.

  3. I've read that the way to validate(check what and how much was done) the Realign around Indels step, is to count/search for the OC Tags in the alignment file. Is there any fast way to do so ? Or do I have to convert the BAM into a SAM and count by running through lines of the alignment ?

  4. Fortunately there exist the "Recommended sets of known sites per tool" which I used so far. But is there any explanation why those sets are recommended ?

Tanks a lot !

Best Answer


  • MaxMax Member

    In the meantime I could solve my third question by using BAMtools which allows to filter for Tags in BAM files.

    However, it would be really great if someone could help me with the remaining questions

  • MaxMax Member

    Hi Geraldine, thats no problem at all ;)

    I guess that the tutorial on VQSR and the article about the Unified Genotyper is enough for the moment. Thanks !

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