The aim of this pipeline is to processed bam files from nf-core/RNAseq and output variants and allele specific expression
The pipeline is built using Nextflow
The main.nf goes through the following steps:
- add read groups ( via picard)
- splitCigarReads (via GATK)
- call variants ( via GATK HaplotypeCaller)
- Variant filtering (via GATK)
- annotate variants for further downstream analysis (via VEP)
- select variants (via GATK)
- allele specific expression (via GATK)
The annotate.nf is added ontop of that (takes variants from filtered variants) and is annotated with vep
Directories output
- haplotypeCaller (raw variants, from haplotypecaller, bziped and indexed)
- VariantFiltration (hard filters applied according to https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq )
- BiallelecVCF (only bialleleic SNVs, for input into allele specific expression)
- VEP (annotated vcf files)
Please note that these files are not filtered and that needs to be done as well