Overcalling BNDs?

[tsneddon]

Hi:
I'm looking at some 30x ONP human genome data and seeing that sniffles appears to overcall variants as translocations (BND) when in fact they contain a duplication. These BND variants are being falsely prioritized in downstream processes. An example is below:

##fileformat=VCFv4.2
##source=Sniffles2_2.2
##command="/nas/longleaf/rhel8/apps/sniffles/2.2/venv/bin/sniffles --input GDN421LR.snf GDN121LR.snf GDN71LR.snf GDN501LR.snf GDN431LR.snf --vcf GDNLR_5multisample_sniffles.vcf"
##fileDate="2024/04/03 15:20:03"
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrM,length=16569>
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Breakend; Translocation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=GT,Description="Genotype filter">
##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
##FILTER=<ID=COV_CHANGE_FRAC,Description="Coverage fractional change filter">
##FILTER=<ID=MOSAIC_AF,Description="Mosaic maximum allele frequency filter">
##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
##FILTER=<ID=STRAND,Description="Strand support filter">
##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GDN421LR GDN121LR GDN71LR GDN501LR GDN431LR
chr7 | 31776967 | Sniffles2.BND.29AM6 | N | ]chr1:65381783]N | 60 | PASS | PRECISE;SVTYPE=BND;SUPPORT=12;COVERAGE=36,24,39,41,41;STRAND=+-;AC=1;STDEV_LEN=0;STDEV_POS=0;SUPP_VEC=10000 | GT:GQ:DR:DV:ID | 0/1:55:23:12:Sniffles2.BND.3BF4S6 | 0/0:0:31:0:NULL | 0/0:0:24:0:NULL | 0/0:0:21:0:NULL | 0/0:0:27:0:NULL

This variant corresponds to the common chr1 ~8kb duplication in gnomAD:
https://gnomad.broadinstitute.org/variant/DUP_CHR1_A70DA16C?dataset=gnomad_sv_r4

The duplication is inserted at around position chr7:31776967.
It is not a translocation.

Is there a way to return less of these spurious BNDs?
Thanks,
Tam

[fritzsedlazeck]

Thanks Tam,
may I ask if you know if this duplciation is tandem or interspersed duplciation ? That could make the difference here.
CNV caller woudl call a region amplified but SV caller would show the molecular connection e.g. it could be that the other copy is connected to chr 1.. ?

Thanks
Fritz