rhocall

Call regions of homozygosity and make tentative UPD calls

Usage

Usage: rhocall [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  aggregate  Aggregate runs of autozygosity from rhofile...
  annotate  Markup VCF file using rho-calls.
  call      Call runs of autozygosity.
  tally     Tally runs of autozygosity from rhofile.

rhocall call

Usage: rhocall call [OPTIONS] VCF

  Call runs of autozygosity.

Options:
  -m, --max_hets FLOAT            Max heterozygotes per Mb in a homozygous
                                  block
  -f, --max_het_fraction FLOAT    Max heterozygotes over homozygotes fraction
                                  in a homozygous block
  -n, --minimum_homs INTEGER      Minimum absolute number of homozygotes to
                                  report a block
  -s, --shortest_block INTEGER    Shortest block
  -u, --flag_upd_at_fraction FLOAT
                                  Flag UPD if homozygous blocks span this
                                  fraction of total chr size
  -k, --individual INTEGER        Index of individual in vcf/bcf, 0-based.
  -s, --block_constant INTEGER    Should be adapted to type of analysis(exome
                                  or genome)
  -v, --verbose
  --help                          Show this message and exit.

rhocall aggregate

Usage: rhocall aggregate [OPTIONS] ROH

  Aggregate runs of autozygosity from rhofile into windowed rho BED file.
  Accepts a bcftools roh style TSV-file with CHR,POS,AZ,QUAL.

Options:
  -q, --quality_threshold FLOAT  Minimum quality trusted to start or end ROH-
                                 windows.
  -v, --verbose
  -o, --output FILENAME
  --help                         Show this message and exit.

rhocall tally

Usage: rhocall tally [OPTIONS] ROH

  Tally runs of autozygosity from rhofile. Accepts a bcftools roh style TSV-
  file with CHR,POS,AZ,QUAL.

Options:
  -q, --quality_threshold FLOAT   Minimum quality that counts towards region
                                  totals.
  -u, --flag_upd_at_fraction FLOAT
                                  Flag UPD if this fraction of chr quality
                                  positions called AZ.
  -v, --verbose
  -o, --output FILENAME
  --help                          Show this message and exit.

rhocall annotate

Usage: rhocall annotate [OPTIONS] VCF

  Markup VCF file using rho-calls. Use BED file to mark all variants in AZ
  windows. Use a bcftools style roh TSV to mark only selected AZ variants.

Options:
  -r FILENAME                     Bcftools roh style TSV file with
                                  CHR,POS,AZ,QUAL.
  -b FILENAME                     BED file with AZ windows.
  -q, --quality_threshold FLOAT   Minimum quality calls that are imported in
                                  region totals.
  -u, --flag_upd_at_fraction FLOAT
                                  Flag UPD if this fraction of chr quality
                                  positions called AZ.
  -v, --verbose
  -o, --output FILENAME
  --help                          Show this message and exit.

Examples

Suggested workflow

Preparation

bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/AF\n' popfreq.vcf.gz | bgzip -c > popfreq.tab.gz

Call ROH with bcftools

Please see the samtools project for installation instructions, and please refer to Narasimhan et al, 2016 regarding method details.

bcftools roh --AF-file popfreq.tab.gz -I sample.bcf > sample.roh

Aggregate ROH calls into windows, and mark up variant file (VCF/BCF)

rhocall aggregate sample.roh -o sample.roh.bed
rhocall annotate -b sample.roh.bed -o sample.rho.vcf sample.bcf

Obtain per chromosome overview

rhocall tally sample.roh -o sample.roh.tally.tsv

Additional usage examples

bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/AF\n' anon-SweGen_STR_NSPHS_1000samples_snp_freq_hg19.vcf.gz | bgzip -c > anon_SweGen_161019_snp_freq_hg19.tab.gz
bcftools roh --AF-file anon_SweGen_161019_snp_freq_hg19.tab.gz -I 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.bcf > 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh
rhocall tally 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh -o 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh.tally.tsv
rhocall annotate -r 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.bcf -o 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh.vcf
rhocall aggregate 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh -o 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh.bed
rhocall annotate -b 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.roh.bed -o 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.rho.vcf 2016-14676_sorted_md_rreal_brecal_gvcf_vrecal_comb_BOTH.bcf

Installation

The cyvcf2 install process appears to be jinxed on certain systems/setups. In practice this means that a chained pip install on a naive system may fail. Installation of each requirement for cyvcf2 prior to installing it appears to work unconditionally.

pip install numpy; pip install Cython
pip install -r requirements.txt
pip install -e .