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Changes between Version 34 and Version 35 of SOP/CallingVariantsRNAseq

v34	v35
3	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	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]
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)~~
	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.]
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7	7	== Using GATK to call variants from RNA-seq reads ==