Changes between Version 59 and Version 60 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/06/17 08:05:13 (7 years ago)
Author:
gbell
Comment:

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  • SOP/CallingVariantsRNAseq

    v59 v60  
    11=== Notes on calling variants in RNA-seq data with GATK ===
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    3 * RNAseq includes reads mapped across splice junctions and is associated with high variability of coverage, so typical variant calling pipelines (for DNA) can lead to lots of false positives and negatives.
    4 * GATK is currently the gold standard for calling variants in RNA-seq data.  See a detailed description of their workflow here:  [https://gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail GATK Variant Calling for RNA-seq]
     3* RNA-seq includes reads mapped across splice junctions and is associated with high variability of coverage, so typical variant calling pipelines (for DNA) can lead to lots of false positives and negatives.
     4* GATK is currently the gold standard for calling variants in RNA-seq data.  See a detailed description of their workflow here
     5  * [https://gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail GATK Best Practices for variant calling on RNAseq]
     6  * [https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 Calling variants in RNAseq] (with sample commands)
    57* A main difference between calling variants in RNA vs DNA sequencing reads with GATK, is for RNA-seq data the [https://github.com/alexdobin/STAR STAR] aligner is used to perform a 2-pass read mapping step, which was shown to have superior SNP sensitivity in a comparison of the most common mapping tools [https://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.html Engström, et al.]
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