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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

vcf file indexing error #27

Closed sandipmkale closed 3 years ago

sandipmkale commented 3 years ago

Hello,

I have indexed the vcf file with $tabix -Cp vcf filename command. But I am getting "Exception: [pixy] ERROR: The vcf is not indexed with tabix." error.

Can you please help.

With best regards

Sandip

ksamuk commented 3 years ago

Hi Sandip,

Did that command produce a .tbi file? I'm not sure if the CSI format (-C flag) is supported by scikit-allel, can you try:

$ tabix your.vcf.gz

Kieran

sandipmkale commented 3 years ago

No. as I mentioned, the chromosome is very big and .tbi can't be generated. I use flag -C to generate .csi. I think, I have to split the chromosome.

Thanks alot.

ksamuk commented 3 years ago

Hi Sandip,

The .csi format isn't supported unfortunately, so you will indeed have to split your chromosome. If scitkit-allel adds support for .csi indexes, we'll be able to supports these in the future. Cheers,

Kieran