treecall

Tree-based joint lineage inference and somatic mutation calling

Treeview requires python2.X

You must have the following installed:
ete2 (note not ete3) (https://github.com/jhcepas/ete/tree/2.3)
pyvcf (https://pyvcf.readthedocs.io)

usage: treecall.py [-h] <command> ...

positional arguments:
  <command>   sub-commands
    tview     view tree
    compare   compare tree topology
    compat    calculate pairwise compatibility between all pairs of sites
    nbjoin    neighbor-joining
    gtype     genotype samples with help of a lineage tree
    annot     annotate lineage tree with genotype calls

optional arguments:
  -h, --help  show this help message and exit

tview

usage: treecall.py tview [-h] [-a STR] [-l FILE] <nwk>

positional arguments:
  <nwk>       input tree in Newick format

optional arguments:
  -h, --help  show this help message and exit
  -a STR      node attributes to print given by a comma separated list
  -l FILE     leaves label
  
output:
  the tree

compare

usage: treecall.py compare [-h] -t FILE [FILE ...] -r FILE

optional arguments:
  -h, --help          show this help message and exit
  -t FILE [FILE ...]  input tree(s), in Newick format
  -r FILE             reference tree, in Newick format
  
output (for each tree):
  tree
  normalized robinson-foulds distance (from 0 to 1)
  compatibility score of the target tree with respect to the source tree (how many edges in reference are found in the source)
  compatibility score of the source tree with respect to the reference tree (how many edges in source are found in the reference)
  sum of differences between two distance matrices / sum of ref matrix
  rstat ?? 

compat

usage: treecall.py compat [-h] [-v INT] <vcf> <output>

positional arguments:
  <vcf>       input vcf/vcf.gz file, "-" for stdin
  <output>    output compatibility matrix

optional arguments:
  -h, --help  show this help message and exit
  -v INT      minimum evidence in Phred scale for a site to be considered, default 60

output:
  ??

nbjoin

usage: treecall.py nbjoin [-h] [-m INT] [-e INT] [-v INT] <vcf> output

positional arguments:
  <vcf>       input vcf/vcf.gz file, "-" for stdin
  output      output basename

optional arguments:
  -h, --help  show this help message and exit
  -m INT      mutation rate in Phred scale, default 80
  -e INT      heterozygous rate in Phred scale, default 30
  -v INT      minimum evidence in Phred scale for a site to be considered, default 60
  
output:
  optimal newick trees (in files) after recursive NNI and recursive rerooting from multiple starting trees (random; nj; partitioning)

gtype

usage: treecall.py gtype [-h] -t FILE [-n INT] [-m INT] [-e INT] <vcf> <output>

positional arguments:
  <vcf>       input vcf/vcf.gz file, "-" for stdin
  <output>    output basename

optional arguments:
  -h, --help  show this help message and exit
  -t FILE     lineage tree
  -n INT      number of sites processed once, default 1000
  -m INT      mutation rate in Phred scale, default 80
  -e INT      heterozygous rate in Phred scale, default 30, 0 for uninformative
  
output:

annot

usage: treecall.py annot [-h] -t FILE <gtcall> <outnwk>

positional arguments:
  <gtcall>    input gtype calls, "-" for stdin
  <outnwk>    output tree in Newick format

optional arguments:
  -h, --help  show this help message and exit
  -t FILE     lineage tree
  
output: