Changes between Version 60 and Version 61 of SOP/CallingVariantsRNAseq
- Timestamp:
- 09/06/17 08:07:42 (7 years ago)
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SOP/CallingVariantsRNAseq
v60 v61 2 2 3 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 4 * GATK is currently the gold standard for calling variants in RNA-seq data. See a detailed description of their workflow here: 5 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 6 * [https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 Calling variants in RNAseq] (with sample commands) 7 * 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.]7 * 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 ([https://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.html Engström, et al.]) to have superior SNP sensitivity in a comparison of the most common mapping tools. 8 8 9 9 == Using GATK to call variants from RNA-seq reads == … … 16 16 17 17 18 '''1 - Run the STAR 2 18 '''1 - Run the STAR 2-pass procedure to map reads to the reference genome.''' 19 19 20 20 '''Index the reference genome for First Pass.'''
