vg construct unsupported variant allele

Question

[Yihang]

I use vg (v1.39.0) construct on a vcf file (VCFv4.2) and hg19 but got the following warning: "warning:[vg::Constructor] Unsupported variant allele "<DEL>"; Skipping variant(s)".

After some simple debugging, I find that it seems that vg cannot support some variants in vcf files with ALTs represented by IDs, such as:

CHROM POS ID REF ALT

chr1 869467 call_2707 G DEL

chr1 1120036 call_1457 G DEL

But will support vcf files with ALTs represented by sequences, such as:

CHROM POS ID REF ALT

chr1 10403 . ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC A

chr1 10415 . ACCCTAACCCTAACCCTAACCCTAAC A

Since the former one is a fairly common vcf format, I wonder if there is some way we can do to make vg constrcut also support that kind of vcf file.

Thanks!

[Pierre Lindenbaum]

save the planet: please, post text rather than screenshots.

[Yihang]

I tried vg construct -S -f, and find that no unsupported variant allele warning appeared anymore. I checked the output .vg file, and find that although this can help encode some ALTs such as <DEL> and <INV>, it is still not able to support all, e.g. <DUP:TANDEM>. More importantly, it seems that vg cannot support all ALTs that are represented by breakends such as G]chr13:81121773], meaning most complex structural variants and inter-chromosomal translocations are removed. Since I am trying to use vg to map reads from some cancer cell types, inter-chromosomal structural variants are actually very important to me. Is there any way to construct a genome graph that has inter-chromosomal SVs? (vg command line or other genome graph construction softwares). Thank you!