genetic_demux/scsplit

Description

scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.

Type

bash_script

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
tag: [ "CB" ]  
sub: [ 10 ]  
ems: [ 30 ]  
output: "$id.$key.output.scSplit_out"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/genetic_demux/scsplit/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--vcf	file	VCF from mixed BAM
--bam	file	mixed sample BAM
--bar	file	barcodes whitelist
--tag	string	tag for barcode
--com	file	common SNVs
--num	integer	expected number of mixed samples
--sub	integer	maximum number of subpopulations in autodetect mode
--ems	integer	number of EM repeats to avoid local maximum
--dbl	double	correction for doublets. There will be no refinement on the results if this optional parameter is not specified or specified percentage is less than doublet rates detected during the run.
--vcf_known	file	known individual genotypes to limit distinguishing variants to available variants, so that users do not need to redo genotyping on selected variants, otherwise any variants could be selected as distinguishing variants.
--geno	boolean_true	generate sample genotypes based on the split result.

Name

Type & Properties

--vcf

file

--bam

file

--bar

file

--tag

string

--com

file

--num

integer

--sub

integer

--ems

integer

--dbl

double

--vcf_known

file

--geno

boolean_true

Output

Name	Type & Properties	Description
--output -o	file output	Output directory
--ref	string	output Ref count matrix
--alt	string	output Alt count matrix
--psc	string	generated P(S\|C)

Name

Type & Properties

--output

-o

file

output

--ref

string

--alt

string

--psc

string