Changes between Version 53 and Version 54 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/06/17 07:36:34 (7 years ago)
Author:
krichard
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOP/CallingVariantsRNAseq

    v53 v54  
    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.
    44* 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]
    5 * 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 Engström, et al.]
     5* 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.]
    66
    77== Using GATK to call variants from RNA-seq reads ==