Problem with vg autoindex with phased VCF

Question

[mirko1998coggi]

Hi, I'm trying to use vg autoindex with the human Chromosome 17 using:

• Homo_sapiens.GRCh37.dna.chromosome.17.fa as REF (downloaded from Ensembl at 1)
• ALL.chr17.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz as Phased Variation File (downloaded from Ensembl at 2)

I'm using the 1.54.00 vg release "Parafada", running the command:

vg autoindex \
  --workflow giraffe \
  -r Homo_sapiens.GRCh37.dna.chromosome.17.fa \
  -v ALL.chr17.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz \
  -p x \
  -V 2

The error I get is:

cannot setRegion on a non-tabix indexed file

And I think this happens inside the function HaplotypeIndexer::parse_vcf.

I also tried to input the .tbi file of the vcf, using -v file.vcf.gz.tbi, but I got this error:

[E::hts_hopen] Failed to open file ALL.chr17.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz.tbi
[E::hts_open_format] Failed to open file "ALL.chr17.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz.tbi" : Exec format error

Crash report for vg v1.54.0 "Parafada"
Stack trace (most recent call last) in thread 1649822:
5    Object "", at 0xffffffffffffffff, in 
4    Object "/usr/lib/x86_64-linux-gnu/libc-2.31.so", at 0x7fbdafd8e352, in __clone Source "../sysdeps/unix/sysv/linux/x86_64/clone.S", line 95, in __clone [0x7fbdafd8e352]
3    Object "/usr/lib/x86_64-linux-gnu/libpthread-2.31.so", at 0x7fbdb04ea608, in start_thread Source "/build/glibc-wuryBv/glibc-2.31/nptl/pthread_create.c", line 477, in start_thread [0x7fbdb04ea608]
2    Object "/usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0", at 0x7fbdafe9886d, in 
1    Object "/home/users/mirko.coggi/vg/bin/vg", at 0x55652eb5fd26, in vg::VGIndexes::get_vg_index_registry()::{lambda(std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool, bool)#4}::operator()(std::vector<vg::IndexFile const*, std::allocator<vg::IndexFile const*> > const&, vg::IndexingPlan const*, vg::AliasGraph&, std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool, bool) const [clone ._omp_fn.0] Source "src/index_registry.cpp", line 654, in _ZZN2vg9VGIndexes21get_vg_index_registryEvENKUlRKSt6vectorIPKNS_9IndexFileESaIS4_EEPKNS_12IndexingPlanERNS_10AliasGraphERKSt3setINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4lessISK_ESaISK_EEbbE2_clES8_SB_SD_SQ_bb._omp_fn.0 [0x55652eb5fd26]
0    Object "/home/users/mirko.coggi/vg/bin/vg", at 0x55652f2ec0a8, in bcf_hdr_read

My question here is double:

1. Is there a way/workflow to autoindex these files?
2. Is there the possibility of creating the GBWT without using the XG graph but only using the FASTA and the VCF?

[Jordan M Eizenga]

You wouldn't want to provide the .tbi index as a VCF. The convention is to have the .tbi file sitting in the same directory as the bgzipped VCF with the same name as the VCF except with .tbi appended (i.e. path/to/vcf_file_name.vcf.gz and path/to/vcf_file_name.vcf.gz.tbi). If you do that, HTSLib should find it automatically.

[mirko1998coggi]

Yes, now it works, thank you.