Duplicate VCF lines from HG002 BAM

[themkdemiiir]

Hello,

I tested your tool on AshkenazimTrio and noticed that vcf_id is common for BND pairs with different quality, and there are duplicate vcf lines.
The reference files I used

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

The Bam and index files used

https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/novoalign_bams/

The duplicate vcf lines. I can also share the VCF file if you want so. Thanks

chr5	58813706	SV_736_1	N	]chr5:58813779]N	50	PASS	SVTYPE=BND;REGIONA=58813706,58813943;REGIONB=58813723,58813779;LFA=0,0;LFB=0,0;LTE=0,0;CTG=GGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAGATATTATTTAACTCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAATGCACACATACAGGCAATCAGGAATGCAGAAATGAATTTACCAAGTTACAAAATGGGTTAACACCCATGGAGCAAGAATCAGATGCATGCCACCAAACACAATTTATTGGCATTTCTTTCTATTTGCAAGAACTTGTATTATTATTGGTTTTCCACCACCTAC	GT:CN:COV:DV:RV:LQ:RR:DR	0/1:2:62.02100840336134,59.54054054054054,59.0:0:0:0.0,0.0:36,46:36,39
chr5	58813706	SV_1066_1	N	]chr5:58813779]N	50	PASS	SVTYPE=BND;REGIONA=58813706,58813755;REGIONB=58813502,58813779;LFA=0,0;LFB=0,0;LTE=0,0;CTG=CCCCCCATGGATCTTTCTACACGCGCGGGGTTGGGTATCTTCTGTGTGCACACTGCTCACCCCCCGTTCTCATAGACAGGTTGTCTAGTCACTCCAAGCACATGCCTTCCTTAGCCATTGTATTGTTAAGTTTTTATGTTTTATTTATATTTATATTTATATATATATATATATATATATATATATATATATATATACACATACACACATATACATATGGTAGAACCACAGCTTTTATCCAAATATAAAATAAACACATGTCAAAGATATTATTTAACTCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAGATATTATTTAAATCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCAGAGGCACAAGTGGATACTCAGTGAACGCAA	GT:CN:COV:DV:RV:LQ:RR:DR	0/1:2:59.32,59.54054054054054,61.881294964028775:0:0:0.0,0.0:36,46:36,39
chr5	58813779	SV_736_2	N	N[chr5:58813706[	50	PASS	SVTYPE=BND;REGIONA=58813706,58813943;REGIONB=58813723,58813779;LFA=0,0;LFB=0,0;LTE=0,0;CTG=GGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAGATATTATTTAACTCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAATGCACACATACAGGCAATCAGGAATGCAGAAATGAATTTACCAAGTTACAAAATGGGTTAACACCCATGGAGCAAGAATCAGATGCATGCCACCAAACACAATTTATTGGCATTTCTTTCTATTTGCAAGAACTTGTATTATTATTGGTTTTCCACCACCTAC	GT:CN:COV:DV:RV:LQ:RR:DR	0/1:2:62.02100840336134,59.54054054054054,59.0:0:0:0.0,0.0:36,46:36,39
chr5	58813779	SV_1066_2	N	N[chr5:58813706[	50	PASS	SVTYPE=BND;REGIONA=58813706,58813755;REGIONB=58813502,58813779;LFA=0,0;LFB=0,0;LTE=0,0;CTG=CCCCCCATGGATCTTTCTACACGCGCGGGGTTGGGTATCTTCTGTGTGCACACTGCTCACCCCCCGTTCTCATAGACAGGTTGTCTAGTCACTCCAAGCACATGCCTTCCTTAGCCATTGTATTGTTAAGTTTTTATGTTTTATTTATATTTATATTTATATATATATATATATATATATATATATATATATATATACACATACACACATATACATATGGTAGAACCACAGCTTTTATCCAAATATAAAATAAACACATGTCAAAGATATTATTTAACTCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCATAGGCTCAAGGGGATATTCAGTGAGATATTATTTAAATCTGGACTTAAAGAAGGGACCAGTAAGATGTTGCAGAGGCACAAGTGGATACTCAGTGAACGCAA	GT:CN:COV:DV:RV:LQ:RR:DR	0/1:2:59.32,59.54054054054054,61.881294964028775:0:0:0.0,0.0:36,46:36,39

[J35P312]

Hello!
Thanks for testing tiddit! There are interesting examples, I see that they are detected through de novo assembly only, and that they are called based on two distinct contigs... I will have a look and see if I can make TIDDIT collapse this kind of calls.

Best regards
Jesper