Discrepancy between using --db and --sqdb built from the same VCF

[fellen31]

Hi,

there seems to be different results when using a --sqdb built from the VCF, and using the VCF directly with --db.

E.g:

svdb --build --files CoLoRSdb.CHM13.v1.1.0.pbsv.jasmine.vcf.gz --prefix colorsdb

svdb --query --query_vcf results/svs/single_sample/HG002.Revio/HG002.Revio_severus.vcf.gz --sqdb colorsdb.db --in_occ AN --out_occ colorsdb_an --in_frq AF --out_frq colorsdb_af|grep "colorsdb_an"
##INFO=<ID=colorsdb_an,Number=1,Type=Integer,Description="The number of occurances of the event in the database">
##INFO=<ID=colorsdb_an,Number=1,Type=Integer,Description="The number of occurances of the event in the database">
##SVDB_version=2.8.2 cmd="/home/felix/.local/bin/mambaforge/envs/svdb/bin/svdb --query --query_vcf results/svs/single_sample/HG002.Revio/HG002.Revio_severus.vcf.gz --sqdb colorsdb.db --in_occ AN --out_occ colorsdb_an --in_frq AF --out_frq colorsdb_af"
chr16   960535  severus_DEL11   N       <DEL>   60      PASS    PRECISE;SVTYPE=DEL;SVLEN=263;END=960798;STRANDS=+-;MAPQ=60;FOUND_IN=severus;colorsdb_an=1;colorsdb_af=1.0        GT:GQ:VAF:hVAF:DR:DV    0/1:273:0.3:0.3,0,0:31:13

vs.

svdb --query --query_vcf results/svs/single_sample/HG002.Revio/HG002.Revio_severus.vcf.gz --db CoLoRSdb.CHM13.v1.1.0.pbsv.jasmine.vcf.gz --in_occ AN --out_occ colorsdb_an --in_frq AF --out_frq colorsdb_af|grep "colorsdb_an"
##INFO=<ID=colorsdb_an,Number=1,Type=Integer,Description="The number of occurances of the event in the database">
##INFO=<ID=colorsdb_an,Number=1,Type=Integer,Description="The number of occurances of the event in the database">
##SVDB_version=2.8.2 cmd="/home/felix/.local/bin/mambaforge/envs/svdb/bin/svdb --query --query_vcf results/svs/single_sample/HG002.Revio/HG002.Revio_severus.vcf.gz --db CoLoRSdb.CHM13.v1.1.0.pbsv.jasmine.vcf.gz --in_occ AN --out_occ colorsdb_an --in_frq AF --out_frq colorsdb_af"
chr16   507738  severus_INS26   N       ACGTTTCCCGTTTTCAGTATCATCTGCCCGTTCTGAGCCATTTGCTCTCTAGCCCTACCATACAGCTGTCATCCTAAGAGT       60      PASS     PRECISE;SVTYPE=INS;SVLEN=81;MAPQ=60;FOUND_IN=severus;colorsdb_an=2762;colorsdb_af=0.000724113   GT:GQ:VAF:hVAF:DR:DV    0/1:38:0.44:0.44,0,0:5:4
chr16   767798  severus_INS36   N       GGGGCACGTGGAGGGGTCGCGTGGAGGAGGGGCGCGTGGAGGGGGCGCGTGGAGGAGGAGGGGCGCATGGGGGGGTGTGGA       60      PASS     IMPRECISE;SVTYPE=INS;SVLEN=81;MAPQ=60;FOUND_IN=severus;colorsdb_an=2762;colorsdb_af=0.000724113 GT:GQ:VAF:hVAF:DR:DV    0/1:108:0.5:0.5,0,0:15:15
chr16   960535  severus_DEL11   N       <DEL>   60      PASS    PRECISE;SVTYPE=DEL;SVLEN=263;END=960798;STRANDS=+-;MAPQ=60;FOUND_IN=severus;colorsdb_an=2762;colorsdb_af=0.019551        GT:GQ:VAF:hVAF:DR:DV    0/1:273:0.3:0.3,0,0:31:13

Seems like when the db gets build, the number of occurrences is not taken from AF, but the number of occurrences in the VCF?