Cellsnp

cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data.

Info

ID: cellsnp
Namespace: genetic_demux

Links

Source

It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo.

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -main-script target/nextflow/genetic_demux/cellsnp/main.nf \
  --help

Run command

Example of params.yaml

# Input
# sam_file: "path/to/file"
# sam_index_file: "path/to/file"
# sam_fileList: "path/to/file"
# regions_vcf: "path/to/file"
# targets_vcf: "path/to/file"
# barcode_file: "path/to/file"
# sample_list: "path/to/file"
# sample_ids: "foo"
genotype: false
gzip: false
print_skip_snps: false
# chrom: "foo"
cell_tag: "CB"
umi_tag: "Auto"
min_count: 20
min_maf: 0.0
doublet_gl: false
# incl_flag: "foo"
# excl_flag: "foo"
count_orphan: false
min_mapq: 20
min_len: 30

# Output
# output: "$id.$key.output.output"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/cellsnp/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Input

Name	Description	Attributes
--sam_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.	file
--sam_index_file	Input SAM/BAM Index file, problem with samFileList.	file
--sam_fileList	A list file containing bam files, each per line, for Mode 1b & 2b.	file
--regions_vcf	A vcf file listing all candidate SNPs, for fetch each variants. If None, pileup the genome. Needed for bulk samples.	file
--targets_vcf	Similar as –regions_vcf, but the next position is accessed by streaming rather than indexing/jumping (like -T in samtools/bcftools mpileup).	file
--barcode_file	A plain file listing all effective cell barcode.	file
--sample_list	A list file containing sample IDs, each per line.	file
--sample_ids	Comma separated sample ids.	string
--genotype	If use, do genotyping in addition to counting.	boolean_true
--gzip	If use, the output files will be zipped into BGZF format.	boolean_true
--print_skip_snps	If use, the SNPs skipped when loading VCF will be printed.	boolean_true
--chrom	The chromosomes to use in integer format 1-22, comma separated	string
--cell_tag	Tag for cell barcodes, turn off with None.	string, default: "CB"
--umi_tag	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.	string, default: "Auto"
--min_count	Minimum aggragated count.	integer, default: 20
--min_maf	Minimum minor allele frequency.	double, default: 0
--doublet_gl	If use, keep doublet GT likelihood, i.e., GT=0.5 and GT=1.5.	boolean_true
--incl_flag	Required flags: skip reads with all mask bits unset.	string
--excl_flag	Filter flags: skip reads with any mask bits set [UNMAP,SECONDARY,QCFAIL (when use UMI) or UNMAP,SECONDARY,QCFAIL,DUP (otherwise)]	string
--count_orphan	If use, do not skip anomalous read pairs.	boolean_true
--min_mapq	Minimum MAPQ for read filtering.	integer, default: 20
--min_len	Minimum mapped length for read filtering.	integer, default: 30

Output

Name	Description	Attributes
--output	Output directory for VCF and sparse matrices.	file, example: "cellsnp_out"

Authors

• Xichen Wu (author)