END and POS do not agree

[asylvz]

1. What were you trying to do?
I'm trying to add 1K genomes variants (merged VCF of each chr into one VCF from the link below using bcftools) to the GRCh38 genome using:

${vg} construct -f -S -a -r ${ref} -v ${vars} > merged_graph.vg

ref= https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz

vars= https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/

2. What did you want to happen?
Generate .vg file with 1K variants embedded (SNP, Indel and SV)

3. What actually happened?
It seems to be working but generates lots of warnings for INS, INV and INS:ME variants such as:

Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] chr10	34746632	HGSV_146800	C	<INS>	0	.	AC=79;AF=0.012336;CM=61.367;AN=6404;AN_EAS=1170;AN_AMR=980;AN_EUR=1266;AN_AFR=1786;AN_SAS=1202;AN_EUR_unrel=1006;AN_EAS_unrel=1008;AN_AMR_unrel=694;AN_SAS_unrel=978;AN_AFR_unrel=1322;AF_EAS=0;AF_AMR=0.00306122;AF_EUR=0;AF_AFR=0.0425532;AF_SAS=0;AF_EUR_unrel=0;MAF_EUR_unrel=0;AF_EAS_unrel=0;MAF_EAS_unrel=0;AF_AMR_unrel=0.00288184;MAF_AMR_unrel=0.00288184;AF_SAS_unrel=0;MAF_SAS_unrel=0;AF_AFR_unrel=0.0408472;MAF_AFR_unrel=0.0408472;AC_EAS=0;AC_AMR=3;AC_EUR=0;AC_AFR=76;AC_SAS=0;AC_EUR_unrel=0;AC_EAS_unrel=0;AC_AMR_unrel=2;AC_SAS_unrel=0;AC_AFR_unrel=54;AC_Het_EAS=0;AC_Het_AMR=3;AC_Het_EUR=0;AC_Het_AFR=76;AC_Het_SAS=0;AC_Het_EUR_unrel=0;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=2;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=54;AC_Het=79;AC_Hom_EAS=0;AC_Hom_AMR=0;AC_Hom_EUR=0;AC_Hom_AFR=0;AC_Hom_SAS=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0;AC_Hom=0;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=1;ExcHet_AMR=0.996936;HWE_EUR=1;ExcHet_EUR=1;HWE_AFR=0.399721;ExcHet_AFR=0.188865;HWE_SAS=1;ExcHet_SAS=1;HWE=1;ExcHet=0.614413;END=34746652;SVTYPE=INS;SVLEN=313;CHR2=chr10;ALGORITHMS=manta;SOURCE=gatksv;EVIDENCE=SR;SPAN=313
END: 34746652  POS: 34746632
Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] chr10	35049936	HGSV_146825	T	<INS:ME:SVA>	0	.	AC=8;AF=0.00124922;CM=61.5853;AN=6404;AN_EAS=1170;AN_AMR=980;AN_EUR=1266;AN_AFR=1786;AN_SAS=1202;AN_EUR_unrel=1006;AN_EAS_unrel=1008;AN_AMR_unrel=694;AN_SAS_unrel=978;AN_AFR_unrel=1322;AF_EAS=0;AF_AMR=0.00306122;AF_EUR=0;AF_AFR=0.00279955;AF_SAS=0;AF_EUR_unrel=0;MAF_EUR_unrel=0;AF_EAS_unrel=0;MAF_EAS_unrel=0;AF_AMR_unrel=0.00432277;MAF_AMR_unrel=0.00432277;AF_SAS_unrel=0;MAF_SAS_unrel=0;AF_AFR_unrel=0.00226929;MAF_AFR_unrel=0.00226929;AC_EAS=0;AC_AMR=3;AC_EUR=0;AC_AFR=5;AC_SAS=0;AC_EUR_unrel=0;AC_EAS_unrel=0;AC_AMR_unrel=3;AC_SAS_unrel=0;AC_AFR_unrel=3;AC_Het_EAS=0;AC_Het_AMR=3;AC_Het_EUR=0;AC_Het_AFR=5;AC_Het_SAS=0;AC_Het_EUR_unrel=0;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=3;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=3;AC_Het=8;AC_Hom_EAS=0;AC_Hom_AMR=0;AC_Hom_EUR=0;AC_Hom_AFR=0;AC_Hom_SAS=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0;AC_Hom=0;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=1;ExcHet_AMR=0.996936;HWE_EUR=1;ExcHet_EUR=1;HWE_AFR=1;ExcHet_AFR=0.994402;HWE_SAS=1;ExcHet_SAS=1;HWE=1;ExcHet=0.995632;END=35049987;SVTYPE=INS;SVLEN=873;CHR2=chr10;ALGORITHMS=melt;SOURCE=gatksv;EVIDENCE=SR;SPAN=873
Warning: inversion SVLEN specifies nonzero length change (complex inversions not canonicalizeable) [canonicalize] chr10	77265130	HGSV_150485	C	<INV>	0	.	AC=5;AF=0.000780762;CM=100.464;AN=6404;AN_EAS=1170;AN_AMR=980;AN_EUR=1266;AN_AFR=1786;AN_SAS=1202;AN_EUR_unrel=1006;AN_EAS_unrel=1008;AN_AMR_unrel=694;AN_SAS_unrel=978;AN_AFR_unrel=1322;AF_EAS=0;AF_AMR=0.00204082;AF_EUR=0.000789889;AF_AFR=0.00111982;AF_SAS=0;AF_EUR_unrel=0.000994036;MAF_EUR_unrel=0.000994036;AF_EAS_unrel=0;MAF_EAS_unrel=0;AF_AMR_unrel=0.00144092;MAF_AMR_unrel=0.00144092;AF_SAS_unrel=0;MAF_SAS_unrel=0;AF_AFR_unrel=0.00075643;MAF_AFR_unrel=0.00075643;AC_EAS=0;AC_AMR=2;AC_EUR=1;AC_AFR=2;AC_SAS=0;AC_EUR_unrel=1;AC_EAS_unrel=0;AC_AMR_unrel=1;AC_SAS_unrel=0;AC_AFR_unrel=1;AC_Het_EAS=0;AC_Het_AMR=2;AC_Het_EUR=1;AC_Het_AFR=2;AC_Het_SAS=0;AC_Het_EUR_unrel=1;AC_Het_EAS_unrel=0;AC_Het_AMR_unrel=1;AC_Het_SAS_unrel=0;AC_Het_AFR_unrel=1;AC_Het=5;AC_Hom_EAS=0;AC_Hom_AMR=0;AC_Hom_EUR=0;AC_Hom_AFR=0;AC_Hom_SAS=0;AC_Hom_EUR_unrel=0;AC_Hom_EAS_unrel=0;AC_Hom_AMR_unrel=0;AC_Hom_SAS_unrel=0;AC_Hom_AFR_unrel=0;AC_Hom=0;HWE_EAS=1;ExcHet_EAS=1;HWE_AMR=1;ExcHet_AMR=0.998979;HWE_EUR=1;ExcHet_EUR=1;HWE_AFR=1;ExcHet_AFR=0.99944;HWE_SAS=1;ExcHet_SAS=1;HWE=1;ExcHet=0.998439;END=77266093;SVTYPE=INV;SVLEN=963;SOURCE=svtools;SPAN=963

5. What data and command can the vg dev team use to make the problem happen?

${vg} construct -f -S -a -r ${ref} -v ${vars} > merged_graph.vg

6. What does running vg version say?

vg 1.61.0