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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

chromosome and zarr_path #33

Closed BaHole closed 3 years ago

BaHole commented 3 years ago

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ksamuk commented 3 years ago

Hi there, sorry you're having this problem. Before we start, can you update to the latest version of pixy? It is probably easiest to do a fresh install by removing your old pixy environment and creating a new one.

BaHole commented 3 years ago

Hi there, sorry you're having this problem. Before we start, can you update to the latest version of pixy? It is probably easiest to do a fresh install by removing your old pixy environment and creating a new one.

Dear Professor, I use the command line :conda install --yes -c conda-forge pixy ,and then it comes out :[pixy] ERROR: The vcf is not indexed with tabix. To fix this, run "tabix [filename].vcf.gz" first

ksamuk commented 3 years ago

Hi there,

The --chromosome flag is used to limit pixy's calculations to specific chromosomes or contigs. When using it, you just need to specify the chromosome/contig names you want as listed in the "CHROM" column of the VCF.

If you do not want calculations for specific chromosome/contigs (i.e. you want estimates for all your chromosome/contigs), you should not include this option (or the --interval_start or --interval_end options).

Also, just a note, in the vast majority of cases, --bypass_invariant_check 'yes' will result in incorrect estimates. You should probably not be using this if your data comes from sequenced individuals.

Hope that helps!

ksamuk commented 3 years ago

Closing this for now, let me know if you run into any other issues.