tapestry-tools

Installation

Install uv:

curl -LsSf https://astral.sh/uv/install.sh | sh
source $HOME/.local/bin/env

Note: prior to running the uv installation commands above, you may need to specify a directory for TMPDIR that you have write access to.

Install tapestry-tools:

uv tool install git+https://github.com/quinlan-lab/tapestry-tools.git

Check that compute-delta-methylation tool is available:

compute-delta-methylation

Imprinting

Test the computation of methylation difference between haplotypes for multiple samples:

# This will run a 2min test (using just 2 samples)
compute-delta-methylation \
    --sample-meth-beds /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/all-cpgs.all-samples.tsv \
    --delta-meth-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/delta-meth.all-samples.test.bed \
    --testing

Compute methylation differences using all samples in the pedigree:

# 25 mins to run for all samples
nohup compute-delta-methylation \
    --sample-meth-beds /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/all-cpgs.all-samples.tsv \
    --delta-meth-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/delta-meth.all-samples.bed \
    > /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/delta-meth.all-samples.log 2>&1 & 

Given the output of compute-delta-methylation (a set of methylation differences between haplotypes for a set of genomic tiles and a set of samples), call imprinted loci:

call-imprinted-loci \
    --delta-meth-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/delta-meth.all-samples.bed \
    --imprinted-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/imprinted-candidates.all-samples.bed

Given a set of loci (e.g., imprinted loci), and a set of samples, compute founder-phased methylation averaged over CpGs in each locus:

compute-methylation-loci \
    --loci-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/imprinted-candidates.all-samples.bed \
    --sample-meth-beds /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/all-cpgs.all-samples.tsv \
    --loci-meth-bed /scratch/ucgd/lustre-labs/quinlan/data-shared/tapestry-tools/CEPH1463.GRCh38.hifi.founder-phased/imprinted-candidates.all-samples.meth.bed

Other general-purpose utilities

Clean genomic coordinates

Convert genomic coordinates from colon-separated format to tab-separated BED format:

clean-coords "chr1:153,617,723-153,617,921"

Output:

chr1	153617723	153617921

Liftover genomic coordinates

Lift over genomic coordinates from one reference genome to another (e.g., hg19 to hg38)

lift-over --old-ref hg19 --new-ref hg38 --coord "chr1:1000000-1000100"