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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg construct fails to load index file #2391

Open dd2019d opened 5 years ago

dd2019d commented 5 years ago

hi,

when i run the following:

vg construct -r Homo_sapiens.GRCh37.dna.primary_assembly.fa -v common_all_20170710.vcf.gz > graph.vg

i am getting:

[tabix++] failed to load the index file.

For the above .fa file i also tried creating index files using

samtools faidx Homo_sapiens.GRCh37.dna.primary_assembly.fa

and, in a separate folder also tried

bwa index Homo_sapiens.GRCh37.dna.primary_assembly.fa

After using samtools and bwa, i am still getting the same failed message as above. Please let me how to resolve this issue? Thanks.

Note: outputs of samtools and bwa were stored in different folders, and tests for each were done separately, too.

ekg commented 5 years ago

You need to index the vcf.gz with tabix

On Tue, Aug 13, 2019, 00:09 dd2019d notifications@github.com wrote:

hi,

when i run the following:

vg construct -r Homo_sapiens.GRCh37.dna.primary_assembly.fa -v common_all_20170710.vcf.gz > graph.vg

i am getting:

[tabix++] failed to load the index file.

For the above .fa file i also tried creating index files using

samtools faidx Homo_sapiens.GRCh37.dna.primary_assembly.fa

and, in a separate folder also tried

bwa index Homo_sapiens.GRCh37.dna.primary_assembly.fa

After using samtools and bwa, i am still getting the same failed message as above. Please let me how to resolve this issue? Thanks.

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