genetic_demux/cellsnp

Description

cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data. It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo.

Input

Name	Type & Properties	Description
--sam_file	file	Indexed sam/bam file(s), comma separated multiple samples. Mode 1a & 2a: one sam/bam file with single cell. Mode 1b & 2b: one or multiple bulk sam/bam files, no barcodes needed, but sample ids and regionsVCF.
--sam_index_file	file	Input SAM/BAM Index file, problem with samFileList.
--sam_fileList	file	A list file containing bam files, each per line, for Mode 1b & 2b.
--regions_vcf	file	A vcf file listing all candidate SNPs, for fetch each variants. If None, pileup the genome. Needed for bulk samples.
--targets_vcf	file	Similar as --regions_vcf, but the next position is accessed by streaming rather than indexing/jumping (like -T in samtools/bcftools mpileup).
--barcode_file	file	A plain file listing all effective cell barcode.
--sample_list	file	A list file containing sample IDs, each per line.
--sample_ids	string	Comma separated sample ids.
--genotype	boolean_true	If use, do genotyping in addition to counting.
--gzip	boolean_true	If use, the output files will be zipped into BGZF format.
--print_skip_snps	boolean_true	If use, the SNPs skipped when loading VCF will be printed.
--chrom	string	The chromosomes to use in integer format 1-22, comma separated
--cell_tag	string	Tag for cell barcodes, turn off with None.
--umi_tag	string	Tag for UMI: UR, Auto, None. For Auto mode, use UR if barcodes is inputted, otherwise use None. None mode means no UMI but read counts.
--min_count	integer	Minimum aggragated count.
--min_maf	double	Minimum minor allele frequency.
--doublet_gl	boolean_true	If use, keep doublet GT likelihood, i.e., GT=0.5 and GT=1.5.
--incl_flag	string	Required flags: skip reads with all mask bits unset.
--excl_flag	string	Filter flags: skip reads with any mask bits set [UNMAP,SECONDARY,QCFAIL (when use UMI) or UNMAP,SECONDARY,QCFAIL,DUP (otherwise)]
--count_orphan	boolean_true	If use, do not skip anomalous read pairs.
--min_mapq	integer	Minimum MAPQ for read filtering.
--min_len	integer	Minimum mapped length for read filtering.

Name

Type & Properties

--sam_file

file

--sam_index_file

file

--sam_fileList

file

--regions_vcf

file

--targets_vcf

file

--barcode_file

file

--sample_list

file

--sample_ids

string

--genotype

boolean_true

--gzip

boolean_true

--print_skip_snps

boolean_true

--chrom

string

--cell_tag

string

--umi_tag

string

--min_count

integer

--min_maf

double

--doublet_gl

boolean_true

--incl_flag

string

--excl_flag

string

--count_orphan

boolean_true

--min_mapq

integer

--min_len

integer

Output

Name	Type & Properties	Description
--output --outDir	file output	Output directory for VCF and sparse matrices.

Name

Type & Properties

--output

--outDir

file

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
cell_tag: [ "CB" ]  
umi_tag: [ "Auto" ]  
min_count: [ 20 ]  
min_maf: [ 0 ]  
min_mapq: [ 20 ]  
min_len: [ 30 ]  
output: "$id.$key.output.cellsnp_out"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.1 \  
  -main-script target/nextflow/genetic_demux/cellsnp/main.nf \  
  -params-file params.yaml

genetic_demux/cellsnp

Input

Output

Run this component

Relationships

Used by

Uses