Template for CRF NextSeq samples

trio_whole_exome_bcbio_crf_template.yaml

+details:
+- algorithm:
+    platform: illumina
+    quality_format: standard
+    aligner: bwa
+    align_split_size: false
+    trim_reads: fastp
+    adapters: [nextera2, polyg]
+    mark_duplicates: true
+    realign: false
+    recalibrate: true
+    effects: vep
+    effects_transcripts: all
+    variantcaller: gatk-haplotype
+    indelcaller: false
+    remove_lcr: true
+    tools_on:
+    - vep_splicesite_annotations
+  analysis: variant2
+  genome_build: hg38
+upload:
+  dir: /scratch/u035/project/trio_whole_exome/analysis/output