Reference Files

GRCh37

Genome

GATK bundle, also available here.

SNV and indel calling

For genomes, use bed file of "callable" regions from GATK's bundle.

For exomes, use bed file corresponding to the platform used for target capture, see documentation on intervals.

Structural variant calling

Delly provides and takes as an argument a file of regions to exclude from variant calling. This excludes telomeres and centromeres from auto- and allosomes as well as any other contig.

For Manta, substract these regions from a bed file of the whole genome to generate a list of regions to include. First clean up the file provided by Delly, since it is not in bed format:

grep -Ev "chr|MT|GL00|NC|hs37d5" human.hg19.excl.tsv > human.hg19.excl.clean.bed
bedtools subtract -a b37.bed -b human.hg19.excl.clean.bed > b37.minusDellyExclude.bed

GRCh38

GATK bundle, also available here.