/tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

Primary LanguageNimMIT LicenseMIT

tiwih: tools i wish(ed) i had

  • fairegions: (fai) generate equal length regions from an fai (for parallelization)
  • combine_slivar_counts: combine counts from slivar for original call and for compound-hets
  • highcov: (bam/cram) find high-coverage regions (~3 minutes per 30X cram)
  • meandepth: (bam/cram) quickly calculate meandepth by sampling (~2 seconds)
  • samplename: (bam/cram) print sample name from readgroup tag
  • setsvalt: (vcf/bcf) set the ALT allele in a manta VCF to left + N + right for paragraph genotyper
  • setref: (vcf/bcf) change ref allele from N to the actual allele.
  • slivar_split_fam: (vcf/bcf) split joint slivar files by family and inheritance mode
  • sum_slivar_counts: sum counts from slivar from same samples split across multiple files/regions
  • vcf2bedpe : convert and SV VCF to simple bedpe