genetic_demux/demuxlet

Description

Demuxlet is a software tool to deconvolute sample identity and identify multiplets when
multiple samples are pooled by barcoded single cell sequencing. If external genotyping data
for each sample is available (e.g. from SNP arrays), demuxlet would be recommended. Be careful
that the parameters on the github is not in line with the newest help version.

Input

Name	Type & Properties	Description
--sam	file	Input SAM/BAM/CRAM file. Must be sorted by coordinates and indexed.
--tag_group	string	Tag representing readgroup or cell barcodes, in the case to partition the BAM file into multiple groups. For 10x genomics, use CB.
--tag_umi	string	Tag representing UMIs. For 10x genomiucs, use UB.
--plp	string	Input pileup format. If the value is a string, it will be considered as the path of the plp file. If the value is boolean true, it will perform dscpileup.
--vcf	file	Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL).
--field	string	FORMAT field to extract the genotype, likelihood, or posterior from
--geno_error_offset	double	Offset of genotype error rate. [error] = [offset] + [1-offset][coeff][1-r2]
--geno_error_coeff	double	Slope of genotype error rate. [error] = [offset] + [1-offset][coeff][1-r2]
--r2_info	string	INFO field name representing R2 value. Used for representing imputation quality.
--min_mac	integer	Minimum minor allele frequency.
--min_call_rate	double	Minimum call rate.
--alpha	string	Grid of alpha to search for (default is 0.1, 0.2, 0.3, 0.4, 0.5)
--doublet_prior	double	Prior of doublet
--sm	string	List of sample IDs to compare to (default: use all).
--sm_list	string	File containing the list of sample IDs to compare.
--sam_verbose	integer	Verbose message frequency for SAM/BAM/CRAM.
--vcf_verbose	integer	Verbose message frequency for VCF/BCF.
--cap_bq	integer	Maximum base quality (higher BQ will be capped).
--min_bq	integer	Minimum base quality to consider (lower BQ will be skipped).
--min_mq	integer	Minimum mapping quality to consider (lower MQ will be ignored).
--min_td	integer	Minimum distance to the tail (lower will be ignored).
--excl_flag	integer	SAM/BAM FLAGs to be excluded.
--group_list	string	List of tag readgroup/cell barcode to consider in this run. All other barcodes will be ignored. This is useful for parallelized run.
--min_total	integer	Minimum number of total reads for a droplet/cell to be considered.
--min_snp	integer	Minimum number of SNPs with coverage for a droplet/cell to be considered.
--min_umi	integer	Minimum number of UMIs for a droplet/cell to be considered.

Name

Type & Properties

--sam

file

--tag_group

string

--tag_umi

string

--plp

string

--vcf

file

--field

string

--geno_error_offset

double

--geno_error_coeff

double

--r2_info

string

--min_mac

integer

--min_call_rate

double

--alpha

string

--doublet_prior

double

--sm

string

--sm_list

string

--sam_verbose

integer

--vcf_verbose

integer

--cap_bq

integer

--min_bq

integer

--min_mq

integer

--min_td

integer

--excl_flag

integer

--group_list

string

--min_total

integer

--min_snp

integer

--min_umi

integer

Output

Name	Type & Properties	Description
--output -o	file output	Output directory
--out	string	demuxlet output file prefix

Name

Type & Properties

--output

-o

file

output

--out

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
tag_group: [ "CB" ]  
tag_umi: [ "UB" ]  
field: [ "GT" ]  
geno_error_offset: [ 0.1 ]  
geno_error_coeff: [ 0 ]  
r2_info: [ "R2" ]  
min_mac: [ 1 ]  
min_call_rate: [ 0.5 ]  
alpha: [ "0.5" ]  
doublet_prior: [ 0.5 ]  
sam_verbose: [ 1000000 ]  
vcf_verbose: [ 1000 ]  
cap_bq: [ 20 ]  
min_bq: [ 13 ]  
min_mq: [ 20 ]  
min_td: [ 0 ]  
excl_flag: [ 3844 ]  
min_total: [ 0 ]  
min_snp: [ 0 ]  
min_umi: [ 0 ]  
output: "$id.$key.output.demux"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/genetic_demux/demuxlet/main.nf \  
  -params-file params.yaml

genetic_demux/demuxlet

Input

Output

Run this component

Relationships

Used by

Uses