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goleft indexcov

Quickly estimate coverage from a whole-genome bam index, providing 16KB resolution

https://github.com/brentp/goleft/tree/master/indexcov

This is useful as a quick QC to get coverage values across the genome.

The module uses the PED and ROC data files to create diagnostic plots of coverage per sample, helping to identify sample gender and coverage issues.

By default, we attempt to only plot chromosomes using standard human-like naming (chr1, chr2... chrX or 1, 2 ... X) but you can specify chromosomes for detailed ROC plots for alternative naming schemes in your configuration with:

goleft_indexcov_config:
  chromosomes:
    - I
    - II
    - III

The number of plotted chromosomes is limited to 50 by default, you can customise this with the following:

goleft_indexcov_config:
  max_chroms: 80

File search patterns​

goleft_indexcov/ped:
  fn: "*-indexcov.ped"
goleft_indexcov/roc:
  fn: "*-indexcov.roc"