SCarborSNV is an efficient algorithm for phylogeny aware genotyping of single cell genomes. SCarborSNV uses dynamic programming to compute the expected evolutionary distance between pairs of cells, then missing information is inferred from an approximate phylogeny built by neighbor joining.
Clone SCarborSNV from github:
git clone https://github.com/coldham10/SCarborSNV.git
To install, in the newly created directory:
make
SCarborSNV takes as input an mpileup file or stream. You must specify the number of cells in the pieup with the -m option.
From a pre-existing mpileup file with 10 cells:
./SCarborSNV -m 10 -p tencells.mpileup
Or, for example, to use a compressed mpileup file:
zcat twentycells.mpileup.gz | ./SCarborSNV -m 20
Command line options are:
| Short option | Long option | Description |
|---|---|---|
-m |
--n-cells |
(Required) Number of cells in the mpileup |
-p |
--pileup-file |
Name of mpileup file to read |
-o |
--vcf-file |
Name of output file. Defaults to SCarborSNV_out.vcf |
--lambda |
Somatic mutation rate | |
--mu |
Germline mutation rate | |
--p-haploid |
Prior probability that any given locus has experienced LOH | |
--p-clonal |
Prior probability that any SNV is public | |
--temp-file |
Name of necessary temp file. By default is written to /tmp. Warning: If running multiple instances of SCarborSNV concurrently you must specify different temp file locations | |
--amp-err |
Probability of a base substitution due to amplification error | |
--p-ado |
Prior probability that a base has experienced allelic dropout | |
--candidate-threshold |
Threshold on posterior probability of alternate allele count being 0 at a locus. Loci with P(aac = 0) < threshold will be considered as candidate mutants. |
The SCarborSNV software is freely available under the GPL v.3.
Copyright 2019 Christopher Oldham
Christopher Oldham
University of Connecticut