10x Genomics
GemCode Genome & Exome

Long Ranger1.3, printed on 11/14/2024

Creating Custom SV Filter Files

The SV Filter BED File

The SV filter file should contain gaps or other regions of the genome that are likely to give false positive SVs, like regions with known or putative assembly issues (eg. unplaced contigs, highly polymorphic regions etc). The SV-calling algorithm makes calls in such regions but marks them as filtered and puts them in the SV candidates file.

The SV filter file included in Long Ranger contains the following sets of regions:

• Assembly gaps: dataset from UCSC. Regions around gaps are likely to be missassembled. Additionally, the length of some gaps might be incorrect in the reference, which can result in deletion calls overlapping the gap.
• Regions that were dropped in the GRCh38 assembly: dataset from UCSC. Only regions with score 0 (dropped in GRCh38) were kept. These regions will be called as deletions when making SV calls against hg19.
• A small set of regions that give consistently spurious signal across samples but are not included in the above categories (eg. the region chr17:43,573,203-44,642,442 which has high homology with several other regions of the genome and is likely missassembled in hg19).
• The decoy sequence and all unplaced contigs.

A SV filter file for a custom reference should follow the BED format. Only the first 4 columns of the file will be used. The filter file should be placed in <refdata folder>/regions/sv_blacklist.bed, where <refdata folder> is the reference folder created by longranger mkref.

Segmental Duplications

Segmental duplications are large scale (>= 1Kb) recent duplications with high (>=90%) sequence identity between copies. Such regions are likely to be missassembled and can potentially lead to incorrect alignments between the duplication copies. Therefore, it is a good idea to mark and filter out SV calls whose breakpoints overlap copies of the same segmental duplication. The UCSC browser provides segmental duplication tracks for some reference assemblies (hg19, GRCh38, mm9, mm10). These should be converted to the BEDPE format and placed in <refdata folder>/regions/segdups.bedpe.