If the input file contains duplicated variants and doesn't have end positions, the GN annotation pipeline fails with error: java.lang.NullPointerException: Cannot invoke "java.lang.Integer.compareTo(java.lang.Integer)" because the return value of "org.genome_nexus.client.GenomicLocation.getEnd()" is null .
GN annotation pipeline can handle duplications with full genomic location, or missing end position with no duplication, but throws errors for duplication AND missing end position.
If the input file contains duplicated variants and doesn't have end positions, the GN annotation pipeline fails with error:
java.lang.NullPointerException: Cannot invoke "java.lang.Integer.compareTo(java.lang.Integer)" because the return value of "org.genome_nexus.client.GenomicLocation.getEnd()" is null.GN annotation pipeline can handle duplications with full genomic location, or missing end position with no duplication, but throws errors for duplication AND missing end position.