Address issue with proper determination of reference allele for certain indels. Generally, can improperly call insertion as deletion when repeated sequence is present inside another occurrence of the same source sequences, as in
NNNA[ACG]CGNN
Summary of number of difference is several manifest inputs
InfiniumCore-24v1-1_A: 5 entries
InfiniumCore-24v1-1_A1: 3 entries
GSA-24v1-0_A6: 149 entries
Main logic regarding reference allele determination is now located in BPMRecord.py under "is_deletion" method. Also added script to download and prepare reference data (scripts/download_reference.sh) to support new tests that require full human genome reference.
Address issue with proper determination of reference allele for certain indels. Generally, can improperly call insertion as deletion when repeated sequence is present inside another occurrence of the same source sequences, as in NNNA[ACG]CGNN
Summary of number of difference is several manifest inputs InfiniumCore-24v1-1_A: 5 entries InfiniumCore-24v1-1_A1: 3 entries GSA-24v1-0_A6: 149 entries
Main logic regarding reference allele determination is now located in BPMRecord.py under "is_deletion" method. Also added script to download and prepare reference data (scripts/download_reference.sh) to support new tests that require full human genome reference.