Dsc pileup

Dsc-pileup is a software tool to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

Info

ID: dsc_pileup
Namespace: genetic_demux

By using pileup files, it would allow us to run demuxlet/freemuxlet pretty fast multiple times without going over the BAM file again

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/dsc_pileup/main.nf \
  --help

Run command

Example of params.yaml 
# Input
# sam: "path/to/file"
tag_group: "CB"
tag_umi: "UB"
exclude_flag: 1796
# vcf: "path/to/file"
# sm: "foo"
# sm_list: "foo"
sam_verbose: 1000000
vcf_verbose: 1000
skip_umi: false
cap_bq: 40
min_bq: 13
min_mq: 20
min_td: 0
excl_flag: 3844
# group_list: "foo"
min_total: 0
min_uniq: 0
min_snp: 0

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

# 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/dsc_pileup/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 Input SAM/BAM/CRAM file. Must be sorted by coordinates and indexed. file
--tag_group Tag representing readgroup or cell barcodes, in the case to partition the BAM file into multiple groups. For 10x genomics, use CB. string, default: "CB"
--tag_umi Tag representing UMIs. For 10x genomiucs, use UB. string, default: "UB"
--exclude_flag SAM/BAM FLAGs to be excluded. integer, default: 1796
--vcf Input VCF/BCF file for dsc-pileup, containing the AC and AN field. file
--sm List of sample IDs to compare to (default: use all). string
--sm_list File containing the list of sample IDs to compare. string
--sam_verbose Verbose message frequency for SAM/BAM/CRAM. integer, default: 1000000
--vcf_verbose Verbose message frequency for VCF/BCF. integer, default: 1000
--skip_umi Do not generate [prefix].umi.gz file, which stores the regions covered by each barcode/UMI pair. boolean_true
--cap_bq Maximum base quality (higher BQ will be capped). integer, default: 40
--min_bq Minimum base quality to consider (lower BQ will be skipped). integer, default: 13
--min_mq Minimum mapping quality to consider (lower MQ will be ignored). integer, default: 20
--min_td Minimum distance to the tail (lower will be ignored). integer, default: 0
--excl_flag SAM/BAM FLAGs to be excluded for SNP overlapping Read filtering Options. integer, default: 3844
--group_list List of tag readgroup/cell barcode to consider in this run. All other barcodes will be ignored. This is useful for parallelized run. string
--min_total Minimum number of total reads for a droplet/cell to be considered. integer, default: 0
--min_uniq Minimum number of unique reads (determined by UMI/SNP pair) for a droplet/cell to be considered. integer, default: 0
--min_snp Minimum number of SNPs with coverage for a droplet/cell to be considered. integer, default: 0

Output

Name Description Attributes
--output Output directory file, example: "demux"
--out dsc-pileup output file prefix string, example: "demuxlet_dsc"

Authors

  • Xichen Wu (author)