hmcnc - Hidden Markov Copy Number Caller
Initially the required packages need to be installed. On our linux cluster the easiest package management software is Anaconda/Miniconda.
- Download shell script (64bit):
https://docs.conda.io/en/latest/miniconda.html#linux-installers
- Run script and setup channels
bash Miniconda3-latest-Linux-x86_64.sh
https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
- Project env - There are many ways to do this but you can set up a project specific environment with all the packages you need.
- bedtools
- samtools
- snakemake
- boost
- R
- gxx
- tabix
conda create --name <proj_env> bedtools samtools snakemake boost R tabix
conda install can be used to further add packages to environment with explicit version numbers.
conda install -n <proj_env> scipy=0.15.0
Always activate the env before attempting a run
conda activate <proj_env>
You might run into a conda init error the first time so run conda init and rerun
Compiling cpp source files
You can run the snakemake based make file:
snakemake -s make.smk.py --config boost=<boost> -j 1 -p
where <boost> is the location of boost_install/include folder.
Most likely {anaconda install}/envs/{proj_env}/include.
./hmcnc
usage: hmcnc <command> [<args>]
Hidden Markov Copy Number Caller command options:
asm: Run a denovo assembly.
aln: Run a reference alignment.
./hmcnc aln -h
usage:
./hmcnc aln --bam <input.bam> --index <ref.index> [<args>]
Run HMM caller on alignment. If available, provide repeat mask annotation (--repeatMask, -r) for the reference used to filter >80 percent repeat content calls.
./hmcnc aln
required arguments:
- --bam BAM Bam file of Alignment, bam index file should be in same dir. (default: None)
- --index INDEX index file of reference/assembly coordinates (default: None)
optional arguments:
- --mq MQ Min MapQ for reads (default: 10)
- --outdir OUTDIR Output directory (default: .)
- --repeatMask REPEATMASK Provide reference based repeat bed file. (default: No)
- --coverage COVERAGE Provide genome-wide coverage, if not specified, caller will calculate mean coverage per contig. (default: No)
- --subread SUBREAD [1|0], Needs subreads filtering or not.(PacBio clr reads) (default: 0)
- -t THREADS, --threads THREADS Threads available (default: 1)
- --epsi EPSI epsilon parameter (default: 90)
- --minL MINL min collapse length (default: 15000)
- --scr SCR Scripts DIR (default: /scratch2/rdagnew/hmmnew/snakemake)
./hmcnc asm
Same as above but without repeat mask step.
- coverage.bins.bed.gz (coverage in 100bp windows)
- copy_number.tsv (copy number profile of whole genome)
- DUPcalls.copy_number.tsv
- DUPcalls.masked_CN.tsv (calls repeat masked)
- DUPcalls.composite.bed (Bookended calls are merged)
- DUPcalls.masked_CN.composite.tsv
- {GENOME}.noclip.pdf (plot of coverage and copy number across WG)
- DELcalls.copy_number.tsv (del calls are naturally recovered)
- CallSummary.tsv
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