Hello vg-team,
I have a graph that I created and indexed using:
vg construct -v vars -r ref -a >graph.vg
vg index -x graph.xg graph.vg
vg index -G graph.gbwt -v vars graph.vg
The VCF used for construction has phased genotypes for all 7 chromosomes, so I would expect 14 haplotype threads. However vg paths reveals many more than that, 945.
vg paths -g graph.gbwt -x graph.xg -E
_thread_ZI284_NC_004353.4_0_1 127100
_thread_ZI284_NC_004353.4_1_1 127104
_thread_ZI284_NC_004354.4_0_0 932781
_thread_ZI284_NC_004354.4_1_0 932778
_thread_ZI284_NC_004354.4_0_1 627525
_thread_ZI284_NC_004354.4_1_1 627553
_thread_ZI284_NC_004354.4_0_2 992875
_thread_ZI284_NC_004354.4_1_2 992884
_thread_ZI284_NC_004354.4_0_3 113038
_thread_ZI284_NC_004354.4_1_3 113036
_thread_ZI284_NC_004354.4_0_4 319932
_thread_ZI284_NC_004354.4_1_4 319953
_thread_ZI284_NC_004354.4_0_5 102680
_thread_ZI284_NC_004354.4_1_5 102686
_thread_ZI284_NC_004354.4_0_6 122150
_thread_ZI284_NC_004354.4_1_6 122160
_thread_ZI284_NC_004354.4_0_7 41509
_thread_ZI284_NC_004354.4_1_7 41514
_thread_ZI284_NC_004354.4_0_8 62633
_thread_ZI284_NC_004354.4_1_8 62637
_thread_ZI284_NC_004354.4_1_9 422021
_thread_ZI284_NC_004354.4_0_9 1177293
...
I see there are two 'main' threads:
_thread_sample_contig_0_x
_thread_sample_contig_1_x
What are the other threads? And what does the 'x' represent? Are they just parts of the collective thread?
Thanks, Cade
•
written
by
cmirchan •
Ambiguities, conflicts or missing data in the phasing information in the VCF will cause the haplotype threads to be broken up. Adding the -P option to your index -G command to force phasing at unphased genotypes may resolve this.
I remade my index with the -P option, but still resulted with 945 paths. Is there anything else I could try?
Sometimes haplotypes contain alternate alleles of overlapping variants that make no sense together (under the vg interpretation of the VCF). By default, this causes a phase break in GBWT construction. With option -o, the construction will use the reference allele for the variant that occurs later in the file in such cases. Together with -P, this option will guarantee haplotype paths spanning the entire contig. However, in some cases the paths will end up using edges that do not exist in the graph.
Hello, i'm letting this answer here for people in futur who may have the same problem.
i solved it by adding '' --discard-overlaps --force-phasing " arguments to the GBWT construction as i had unphased VCF file (Documentation here)
The vg paths then showed 20 haplotypes for my 10 samples
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