pcingola/SnpEff

MT chromosome data is not available

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algarsi3 commented

Describe the issue
I would like to annotate VCF's using the MT chromosome, but I cannot find its sequence in any assembly I downloaded.

To Reproduce

  1. SnpEff version: 5.2c (2024-04-09)5.2c (2024-04-09)
  2. Genome version: Several I downloaded, namely:
    • GRCh38.mane.1.2.ensembl
    • GRCG38.99
    • GRCh38.86
    • GRCh37.p13
    • GRCh37.87
    • hg38
    • hg19
  3. SnpEff full command line: java -jar snpEff.jar download -d {corresponding database}
  4. Output / Error message: No error, just missing information

Expected behavior
To find the MT chr sequence in the data

What database should I download in order to find the MT chr sequence?