somalier: extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF
Quick Start
somalier makes checking any number of samples for identity easy directly from the alignments or from jointly-called VCFs:
The first step is to extract sites. For VCF just use:
somalier extract -d extracted/ --sites sites.vcf.gz -f /data/human/g1k_v37_decoy.fa $cohort.vcf.gz
with a sites file from releases
For BAM or CRAM, use: This is parallelizable by sample via cluster or cloud, but here, using a for loop:
for f in *.cram; do
somalier extract -d extracted/ --sites sites.vcf.gz -f /data/human/g1k_v37_decoy.fa $f
done
--sites is a VCF of known polymorphic sites in VCF format. A good set is provided in
the releases but any set of common variants will work.
⚠️ somaliercan work on GVCF and individual VCFs, but it is recommended to extract from bam/cram when possible. It is also good to extract from a jointly-called VCF/BCF when only looking within that cohort. While extracting from a single-sample VCF is possible (with --unknown) and GVCF is also supported, these options are less accurate and more prone to problems.
The next step is to calculate relatedness on the extracted data:
somalier relate --ped $pedigree extracted/*.somalier
This will create text and interactive HTML output (similar to peddy) that makes it fast and easy to detect mismatched samples and sample-swaps.
Example output is here
Note that the somalier relate command runs extremely quickly (< 2 seconds for 600 samples and ~1 minute for 4,500 samples) so it's possible
to add/remove samples or adjust a pedigree file and re-run iteratively.
For example to add the n + 1th samples, just run somalier extract on the new sample and then re-use
the already extracted data from the n original samples.
For huge sample-sets, if you run into a bash error for argument list too long, you can pass the somalier files as quoted
glob strings like: "/path/to/set-a/*.somalier" "/path/to/set-b/*.somalier".
Example Output
Infer
somalier can also infer first-degree relationships (parent-child) when both-parents
are present and can often build entire pedigrees on high-qualty data. To do this, use
somalier relate --infer ... and the samples.tsv output will be a pedigree file
indicating the inferred relationships.
See wiki for more detail.
Usage
The usage is also described above. Briefly, after downloading the somalier binary and a sites vcf from the releases run:
somalier extract -d cohort/ --sites sites.hg38.vcf.gz -f $reference $sample.bam
for each sample to create a small binary file of the ref and alt counts for the variants listed in sites.hg38.vcf.gz.
for a vcf, run:
somalier extract -d cohort/ --sites sites.hg38.vcf.gz -f $reference $cohort.bcf
somalier can extract from a multi or single-sample VCF or a GVCF. This will be much faster, in cases where it's available,
this would look like:
somalier extract -d extracted/ --sites sites.vcf.gz -f /data/human/g1k_v37_decoy.fa joint.vcf.gz
following this, there will be a $sample.somalier file for each sample in the joint.vcf.gz
Note that somalier uses the AD field to extract depth information. If that FORMAT field is not present in the
header, then it will use the genotypes only and use a total depth of 20 (10,10 for heterozygote), etc.
Then run:
somalier relate --ped $pedigree_file cohort/*.somalier
This will create an html file for QC in a few seconds.
Note that if a new sample is added to the cohort, it's only necessary to perform
the extract step on that sample and then run the (fast) relate step again with all
of the extracted files.
Extended Usage
For each command of somalier, extended parameters are listed in --help of each subcommand.
$./somalier --help
Commands:
extract : extract genotype-like information for a single sample from VCF/BAM/CRAM.
relate : aggregate `extract`ed information and calculate relatedness among samples.
ancestry : perform ancestry prediction on a set of samples, given a set of labeled samples
find-sites : create a new sites.vcf.gz file from a population VCF (this is rarely needed).
somalier extract
extract genotype-like information for a single-sample at selected sites
Usage:
somalier extract [options] sample_file
Arguments:
sample_file single-sample CRAM/BAM/GVCF file or multi/single-sample VCF from which to extract
Options:
-s, --sites=SITES sites vcf file of variants to extract
-f, --fasta=FASTA path to reference fasta file
-d, --out-dir=OUT_DIR path to output directory (default: .)
--sample-prefix=SAMPLE_PREFIX
prefix for the sample name stored inside the digest
somalier relate
calculate relatedness among samples from extracted, genotype-like information
Usage:
somalier relate [options] [extracted ...]
Arguments:
[extracted ...] $sample.somalier files for each sample. the first 10 are tested as a glob patterns
Options:
-g, --groups=GROUPS optional path to expected groups of samples (e.g. tumor normal pairs).
specified as comma-separated groups per line e.g.:
normal1,tumor1a,tumor1b
normal2,tumor2a
--sample-prefix=SAMPLE_PREFIX
optional sample prefixes that can be removed to find identical samples. e.g. batch1-sampleA batch2-sampleA
-p, --ped=PED optional path to a ped/fam file indicating the expected relationships among samples.
-d, --min-depth=MIN_DEPTH only genotype sites with at least this depth. (default: 7)
--min-ab=MIN_AB hets sites must be between min-ab and 1 - min_ab. set this to 0.2 for RNA-Seq data (default: 0.3)
-u, --unknown set unknown genotypes to hom-ref. it is often preferable to use this with VCF samples that were not jointly called
-i, --infer infer relationships (https://github.com/brentp/somalier/wiki/pedigree-inference)
-o, --output-prefix=OUTPUT_PREFIX
output prefix for results. (default: somalier)
Note that for large cohorts, by default, somalier relate will subset to interesting sample-pairs so as not to
balloon the size of the output. By default, pairs that are expected to be unrelated and have a relatedness <= 0.05.
If you wish to force all samples to be reported, then set the environment variable SOMALIER_REPORT_ALL_PAIRS to any non-empty
value, e.g. export SOMALIER_REPORT_ALL_PAIRS=1
find-sites
To create a set of new sites, use somalier find-sites on a population VCF. More info on this tool is available in the wiki
Install
get a static binary from here
Users can also get a docker image here which contains htslib and a somalier binary ready-for-use.
How it works
somalier takes a list of known polymorphic sites. Even a few hundred (or dozen) sites
can be a very good indicator of relatedness. The best sites are those with a population
allele frequency close to 0.5 as that maximizes the probability that any 2 samples will differ.
A list of such sites is provided in the releases
for GRCh37 and hg38.
In order to quickly calculate genotypes at these sites, somalier assays the exact base.
The extraction step is done directly from the bam/cram files 1 sample at a time.
The relate step is run on the output of the extract commands. It runs extremely quickly
so that new samples can be added and compared. It uses 3 bit-vectors per sample for hom-ref,
het, hom-alt. Each bitvector is a sequence of 64 bit integers where each bit is set if
the variant at that index in the sample is for example, heterozygous. With this setup,
we can use fast bitwise operations and popcount
hardware instructions to calculate relatedness extremely quickly.
For each sample-pair, it reports:
- IBS0 -- the number of sites where one sample is hom-ref and another is hom-alt
- IBS2 -- the number of sites where the samples have the same genotype
- shared-hets -- the number of sites where both samples are heterozygotes
- shared-hom-alts -- the number of sites where both samples are homozygous alternate
These are used to calculate relatedness and a measure of relatedness that is unaffected by loss-of-heterozygosity that is often seen in some cancers. The interactive output allows toggling between any of these measures.
It also reports depth information and the count of HET, HOM_REF, HOM_ALT, and unknown genotypes for each sample
along with a number of metrics that are useful for general QC.
Example
Here, each point is a pair of samples. We can see that the expected identical sample-pairs (e.g. tumor-normal pairs) specified by the user and drawn in red mostly cluster together on the right. Unrelateds cluster on the lower left. The sample-swaps are the blue points that cluster with the red. In the somalier output, the user can hover to see which sample-pairs are involved each point
Ancestry Estimate
somalier can predict ancestry on a set of query samples given a set of labelled samples. You can read more about this in the wiki
Usage
Usage is intentionally very simple and running somalier extract or somalier relate will give sufficient help for nearly
all cases.
By default somalier will only consider variants that have a "PASS" or "RefCall" FILTER. To extend this list, set
the environment variable SOMALIER_ALLOWED_FILTERS to a comma-delimited list of additional filters to allow.
by default sites with an allele balance < 0.01 will be considered homozygous reference. To adjust this, use e.g. :
SOMALIER_AB_HOM_CUTOFF=0.04 somalier relate ...
Other Work
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499645/
https://academic.oup.com/bioinformatics/article/33/4/596/2624551
Acknowledgement
This work was motivated by interaction and discussions with Preeti Aahir and several early users who provided valuable feedback.