SVAFotate supporting files and data

Here we provide input BED files for use with SVAFotate that are derived from the SV datasets generated by CCDG, gnomAD, and 1000G. These are provided for GRCh37 and GRCh38 reference builds and the files are named: SVAFotate_core_SV_popAFs.GRCh37.bed.gz SVAFotate_core_SV_popAFs.GRCh38.bed.gz Additional data files are included that contain the information necessary to generate the NeoSeq analysis as described in the SVAFotate manuscript. These correspond to SV calls made by the variant callers Smoove and Manta and annotations provided by SVAFotate using the provisional BED files listed above and also a custom NeoSeq-specific BED file. These files are named: manta_proband_GTs_AFs_NeoSeq_BED.txt manta_proband_GTs_AFs_provisional_BED.txt smoove_proband_GTs_AFs_NeoSeq_BED.txt smoove_proband_GTs_AFs_provisional_BED.txt