Route: rna-snv
Variant detection in RNA-seq data. Can be run following rna-star.
Segments:
- Trim adapters and low quality bases (Trimmomatic).
- Align to the reference genome (STAR).
- Align to other species and common contaminants (fastq_screen).
- Generate normalized genome browser tracks.
- Remove duplicate reads (Sambamba).
- Realign and recalibrate (GATK).
- Determine depth of coverage (GATK).
- Call point mutations and small insertions/deletions (GATK HaplotypeCaller and LoFreq).
For somatic variant detection, follow with wes-pairs-snv.
Usage
Set up a new analysis (common across all routes). If running for the first time, check the detailed usage instructions for an explanation of every step.
cd <project dir>
git clone --depth 1 https://github.com/igordot/sns
sns/generate-settings <genome>
sns/gather-fastqs <fastq dir>
Run rna-snv route.
sns/run rna-snv
Check for potential problems.
grep "ERROR:" logs-sbatch/*