Entering edit mode
3 days ago
zhengluo
•
0
vg construct --reference ref.fa --vcf test.vcf.gz --alt-paths-plain --handle-sv --flat-alts --progress -t 100 > test.vg
vg index --xg-name test.xg --xg-alts test.vg --threads 100 --progress
vg index test.vg -v test.vcf.gz -G test.gbwt --threads 100
When I used the above workflow for graph construction and indexing, the following error was reported. However, when I replaced vg construct --alt-paths-plain with vg construct --alt-paths, no error occurred. How can I resolve this issue? I want to use the ID column in the VCF file to represent the sites instead of the SHA1 hash.
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 22cf426d1370f64ba07a402013bd74444b09d07b at chr10:135709 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for aee5c618c188582172ad1998af9cc8b1c2b8ffa9 at chr10:137849 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for d443fca6a0117deed478f3173ba2452afd05433b at chr10:174502 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 54a75dd4b031c58b71d1e10581bf0a5769b56a80 at chr10:174503 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 1a1a042ec0c2d2a42a953052b0071de2371bb0e1 at chr10:268317 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 268521ba5aae94d259500e70f30261cb11c9561d at chr10:272677 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 9e30a7ac6d9a1ec7ee757c253ff84d50c2bcca99 at chr10:289795 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for d7ad36356bb8c852510cc0e13b3b70974826f4e6 at chr10:289815 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for 6390f3a5034a250b23498d38475e66988faa4acc at chr10:483098 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] alt and ref paths for de75e8024cb96a93da114eec7132ef31587c1078 at chr10:483657 missing/empty! Was the variant skipped during construction?
warning: [HaplotypeIndexer::parse_vcf] suppressing further missing variant warnings
warning: [HaplotypeIndexer::parse_vcf] Found 2713/0 variants in phasing VCF but not in graph! Do your graph and VCF match?
