pedrel

• add new pedrel command to report kinship value for samples from a pedigree file

Installation

grab the static binary , or use docker via brentp/somalier:v0.3.1

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

v0.3.0

More lenient sex inference

Installation

grab the static binary , or use docker via brentp/somalier:v0.3.0

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

v0.2.19

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