v0.2.19

v0.2.19

• [relate/infer] fix check that would prevent some inference (#123 thanks @equinne5 for reporting and providing test-case)

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.19

sites files

a T2T sites by @kpalin
sites.chm13v2.T2T.vcf.gz
)

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

Different coordinates from above files: sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

find_sites fixes

v0.2.18

• [find_sites] handle empty alternate alleles (#121 thanks @johanneskoester for reporting)
• [find_sites] add --output-vcf option

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.18

sites files

a T2T sites by @kpalin
sites.chm13v2.T2T.vcf.gz
)

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

Different coordinates from above files: sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

missing RG

• allow setting bam sample name via ENV when RG is missing (#115)

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.17

sites files

a T2T sites by @kpalin
sites.chm13v2.T2T.vcf.gz
)

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

Different coordinates from above files: sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

v0.2.16

This makes find-sites faster and less buggy (only needed if you wish to create your own sites files).

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.16

sites files (unchanged from previous releases except for T2T)

a new T2T sites file matching those for hg38 and GRCh37 was created by @kpalin
sites.chm13v2.T2T.vcf.gz
)

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

Different coordinates from above files: sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

minor find-sites fix

this is a minor release that fixes problems with previous binary.

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.15

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

v0.2.14

this is a minor release. with small usability improvements. see below for details:

changes

• minor fixes to find-sites
• allow setting env variable SOMALIER_REPORT_ALL_PAIRS to force reporting of all sample-pairs (#76)
• improve readme (via @zztin)

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.14

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

trio inference fix

v0.2.13

• add "Heterozygosity rate" as a per-sample metric to the html output. (Thanks Irenaeus and Kelly for the suggestion)
• fix inference for some cases. obvious parent-child pairs were sometimes missed.

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.13

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

scaling IBS

v0.2.12

• add checkbox to HTML to scale IBS0, IBS2, etc by number of sites shared by the samples. this almost always
  results in a scaling that is better across (pairs of) samples.
• ancestry: allow globs for ancestry files (#59)

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.12

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

v0.2.11

This release adds small changes, except that the relatedness calculation has been corrected. It worked for most cases except when the number of sites was extremely low. It is now more accurate in more cases. This was reported by @fgvieira . See below for full release details.

v0.2.11

• more informative error message on bad sample name (#53)
• allow setting SOMALIER_AB_HOM_CUTOFF to change which calls are considered hom-ref (#56)
• adjust (fix) relatedness calculation which was off when the number of shared sites was low (#55).
  many thanks to @fgvieira who found and diagnosed this problem. This change adds a hets_ab column
  which is the count of times sample a was het and b was not unknown + the times sample b was het
  and a was not unknown; this is mostly not needed except to (re) calculate relatedness but is reported
  in the text output for completeness.

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.11

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX

sites file optimized for RNA-Seq, bug-fixes and ancestry improvements

v0.2.10

• added a new sites file that includes sites likely to be expressed in GTeX to improve kinship estimation in RNA-Seq data (see below for link to new sites file).
• fix extra output column in pairs.tsv (#47)
• change output file name of ancestry to include "somalier"
• fix for gvcf with empty alts (#46)
• add include regions and exclude sites to find-sites
• add --min-ab option to somalier relate to limit het sites to min_ab..(1-min_ab). default is 0.3
• html output for sample plot defaults to number of het sites on X (was hom-alt)
• better estimates in somalier ancestry when incoming samples are different ancestry from training (thousand genomes samples)

example output is now at: https://brentp.github.io/somalier/ex.html
and: https://brentp.github.io/somalier/ex.somalier-ancestry.html

Installation

grab the static binary , or use docker via brentp/somalier:v0.2.10

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

sites.hg38.rna.vcf.gz only includes sites likely to be expressed in GTeX