Resources.md

Resource files on sdf-cs1 (ultra2)

Exome targets

The TWIST target BED file is at: /home/u035/u035/shared/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed

To generate the target BED file, first copy the file Twist_Exome_RefSeq_targets_hg38.bed from NHS Clinical Genetics Services to /home/u035/u035/shared/resources/exome_targets, then pad it by 15bp each side.

cd /home/u035/u035/shared/resources/exome_targets
PATH=/home/u035/u035/shared/software/bcbio/tools/bin:$PATH

bedtools slop -g $REFERENCE_GENOME.fai -i Twist_Exome_RefSeq_targets_hg38.bed -b 15 | \
  bedtools merge > Twist_Exome_RefSeq_targets_hg38.plus15bp.bed

Other exome targets

Retained for reference in /home/u035/u035/shared/resources/exome_targets/archive.

Resources for variant prioritization

See Setup for variant prioritization.