v0.1.5

v0.1.5

• add experimental contamination estimate. this simply prints to stderr the sample and
  inferred source (another sample) of contamination along with the estimated level of
  contamination and the number of sites used to estimate it.
• fix threading bug with large numbers of samples.
• more lenient ped file parsing ("Female" will be recognized in sex column and
  "Affected" in phenotype column).
• the html output now allows selecting a single sample to be highlighted in the plot
  this allows finding a sample of interest in a large cohort.
• the output now includes a new metric for proportion of sites with an allele balance

  0.02 and < 0.2 or > 0.8 and < 0.98. this turns out to be a nice QC (high is bad)

• for low coverage or targetted sites, sometimes nan values would stop the entire
  html page from working; this has been fixed.
• make sure all reported relationships are plotted in correct colors (#14)
• plotting fixes (#15)

Install

This release comes with 2 linux binaries:

• somalier_static is a completely static binary; just wget, chmod+x (get a sites file) and go.
• somalier_shared requires htslib (and libhts.so). use this binary if you need to access S3 or https files.

Sites files

hg38:

sites.hg38.vcf.gz
sites.chr.hg38.vcf.gz (for hg38 VCFs with "chr" prefix)

GRCh37

sites.vcf.gz