genetic_demux/dsc_pileup

Description

Dsc-pileup is a software tool to pileup reads and corresponding base quality
for each overlapping SNPs and each barcode. By using pileup files,
it would allow us to run demuxlet/freemuxlet pretty fast multiple times
without going over the BAM file again.

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
tag_group: [ "CB" ]  
tag_umi: [ "UB" ]  
exclude_flag: [ 1796 ]  
sam_verbose: [ 1000000 ]  
vcf_verbose: [ 1000 ]  
cap_bq: [ 40 ]  
min_bq: [ 13 ]  
min_mq: [ 20 ]  
min_td: [ 0 ]  
excl_flag: [ 3844 ]  
min_total: [ 0 ]  
min_uniq: [ 0 ]  
min_snp: [ 0 ]  
output: "$id.$key.output.demux"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/genetic_demux/dsc_pileup/main.nf \  
  -params-file params.yaml

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.
--exclude_flag	integer	SAM/BAM FLAGs to be excluded.
--vcf	file	Input VCF/BCF file for dsc-pileup, containing the AC and AN field.
--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.
--skip_umi	boolean_true	Do not generate [prefix].umi.gz file, which stores the regions covered by each barcode/UMI pair.
--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 for SNP overlapping Read filtering Options.
--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_uniq	integer	Minimum number of unique reads (determined by UMI/SNP pair) for a droplet/cell to be considered.
--min_snp	integer	Minimum number of SNPs with coverage for a droplet/cell to be considered.

Name

Type & Properties

--sam

file

--tag_group

string

--tag_umi

string

--exclude_flag

integer

--vcf

file

--sm

string

--sm_list

string

--sam_verbose

integer

--vcf_verbose

integer

--skip_umi

boolean_true

--cap_bq

integer

--min_bq

integer

--min_mq

integer

--min_td

integer

--excl_flag

integer

--group_list

string

--min_total

integer

--min_uniq

integer

--min_snp

integer

Output

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

Name

Type & Properties

--output

-o

file

output

--out

string