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The Chromosome name is not always processed correctly by tabix and samtools #2

@FadyMohareb

Description

@FadyMohareb

To reproduce:

  • Open the Human Genome instance
  • Zoom in Chromosome 1
  • samtools and tabix doesn't work with some of the added track and throw the following error:
    Command: /usr/local/bin/samtools faidx /Users/fmohareb/Dropbox/Manuscripts/SampleData/Homo_sapiens.GRCh38.dna.chromosome.1.fa chr1:202801001-202999000 | tail -n+2
    stderr: [W::fai_get_val] Reference chr1:202801001-202999000 not found in file, returning empty sequence

and

Command: /usr/local/tabix /Users/fmohareb/Dropbox/Manuscripts/SampleData/CEU.low_coverage.2010_09.genotypes.vcf.gz 1:7767968-7932036
stderr: [W::fai_get_val] Reference chr1:7767001-7933000 not found in file, returning empty sequence
[faidx] Failed to fetch sequence in chr1:7767001-7933000

Not sure if this is relation to the uploaded files not being preprocessed with the right chromosome name, or is it an internal Genoverse error

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