Found multiple references in the fasta file

[snashraf]

$ variantstore construct -r /gpfs/ngsdata/ref_data/Homo_sapiens/hs37d5/Sequences/BWAIndex/hs37d5.fa -v 210811_WGS30_B1.vcf.gz -p KF_SDR
[2021-09-07 09:16:39.170] [info] Creating variant graph
Found multiple references in the fasta file
Aborted

Any idea why I am getting this error?

Regards,
Najeeb

[prashantpandey]

Hi @snashraf ,

VariantStore expects a single reference in the fasta file corresponding to the VCF file. The error you are seeing should be because there are multiple references in the fasta file that you are using.

Thanks,
Prashant

[snashraf]

Hi @prashantpandey

I have used the same reference file for variant calling so I am not sure why it's saying multiple fasta files. It's a standard hs37d5 file.

Regards,
Najeeb

[prashantpandey]

Hi @snashraf , does the fasta file contain multiple chromosomes?

You will have to create the fasta file for individual chromosomes. For example, you can look at the 1000 Genomes dataset. There VCF files are available for individual chromosomes and the fasta file should also contain the reference for a single chromosome.

Thanks,
Prashant

[snashraf]

Yes ! It has multiple choromosome. Regards, Najeeb

…

On Wed, 8 Sep 2021, 20:54 Prashant Pandey, ***@***.***> wrote: Hi @snashraf <https://github.com/snashraf> , does the fasta file contain multiple chromosomes? You will have to create the fasta file for individual chromosomes. For example, you can look at the 1000 Genomes dataset. There VCF files are available for individual chromosomes and the fasta file should also contain the reference for a single chromosome. Thanks, Prashant — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBFINZTMBTNPCY4GMQYZL3UA6POVANCNFSM5DRU2JMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.