Skip to content

pedigree inference and better handling of identical samples
Compare
Choose a tag to compare
@brentp brentp released this 24 Feb 17:39
· 72 commits to master since this release
v0.2.8
a0fd075

v0.2.8

  • html output has a list of pre-sets to auto-select informative X, Y axes for the sample plot

  • add --infer flag to somalier relate to allow inferring relatedness.
    this accompanies a change in the .samples.tsv output so that it can be used as a pedigree file

  • add --sample-prefix option to extract and corresponding (multi-)option to relate. So, given
    a cohort with DNA and RNA where samples have identical IDs (SM tags) in the DNA and RNA, can use
    somalier as:

    somalier extract -d DNA --sample-prefix DNA- ...
somalier extract -d RNA --sample-prefix RNA- ...

somalier relate --sample-prefix DNA- --sample-prefix RNA- DNA/*.somalier RNA/*.somalier ...

    and it will show the samples that have
    matching IDs after stripping the prefixes as "identical".

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.8

sites files (unchanged from previous releases)

These sites files are build-specific, but as of this release, once the sites are extracted, the resulting somalier files can be used to compare samples even across genome builds.

sites.hg19.vcf.gz
sites.hg38.nochr.vcf.gz
sites.GRCh37.vcf.gz
sites.hg38.vcf.gz

Assets 3
Loading