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

本数据集提供可配合SVAFotate工具使用的输入BED文件（BED），这些文件源自CCDG、gnomAD及1000G生成的结构变异（Structural Variant, SV）数据集。本数据集针对GRCh37与GRCh38两种参考基因组构建版本提供对应文件，文件命名如下：
SVAFotate_core_SV_popAFs.GRCh37.bed.gz
SVAFotate_core_SV_popAFs.GRCh38.bed.gz

此外本数据集还包含额外数据文件，这些文件携带了SVAFotate研究论文中所述NeoSeq分析所需的全部信息。这些文件对应由变异检出工具Smoove与Manta生成的结构变异检出结果，且包含SVAFotate基于上述临时BED文件及专属NeoSeq定制BED文件所生成的注释信息。文件命名如下：
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