Workflow for SNP calling from GTEX RNA-seq data using the GATK Best Practices pipeline.
The RNA-seq data obtained (.bam files, not provided here) were from the GTEX project, V8. They had been aligned to the reference genome GRCh38 using STAR v2.5.3a.
The industry-standard GATK Best Practices was closely followed (with the help of the UCLA workshop) with the addition of SplitNCigar for splitting alignment overlapping exon/intron junctions and rescaling mapping quality. Hard filtering was performed rather than using VQSR (as there is not yet the RNAseq training/truth resources that are needed).
- GATK pipeline: https://gatk.broadinstitute.org/hc/en-us
- UCLA youtube tutorial 1: https://www.youtube.com/watch?v=xLm3Le0rfYQ
- UCLA youtube tutorial 2: https://www.youtube.com/watch?v=hRsjy1Z8QDA&t=552s
- RNA-calling: https://link.springer.com/protocol/10.1007/978-1-0716-2293-3_13