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
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
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
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"