Changes between Version 32 and Version 33 of SOP/CallingVariantsRNAseq


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Timestamp:
08/16/17 13:12:09 (8 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v32 v33  
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    33* 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
     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 RNA-seq]
    55* A main difference between calling variants in RNA vs DNA sequencing reads with GATK, is for RNA-seq data the 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)
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