Argument Name

Summary

Default Value

sequencing-center

The sequencing center from which the data originated

MSKCC

sample

The name of the sequenced sample.(Required)

run-date

Date the run was produced, to insert into the read group header (Iso8601Date)

read-group-id

Argument Name

Summary

Default Value

fgbio_fastq_to_bam_umi-tag

Tag in which to store molecular barcodes/UMIs.

fgbio_fastq_to_bam_sort

If true, query-name sort the BAM file, otherwise preserve input order.

fgbio_fastq_to_bam_input

Fastq files corresponding to each sequencing read ( e.g. R1, I1, etc.). Please refer to the template file to get this correct.

read-structures

Argument Name

Summary

Default Value

gatk_merge_sam_files_output_file_name

SAM or BAM file to write the merged result to (Required)

merge_sam_files_sort_order

Sort order of output file

queryname

Argument Name

Summary

Default Value

unpaired_fastq_file

unpaired fastq output file name

UBG_picard_SamToFastq_R1_output_fastq

Read1 fastq.gz output file name for uncollapsed bam generation (Required)

UBG_picard_SamToFastq_R2_output_fastq

Read2 fastq.gz output file name for uncollapsed bam generation (Required)

BC_gatk_sam_to_fastq_output_name_R1

Argument Name

Summary

Default Value

fastp_unpaired1_output_file_name

For PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it.

fastp_unpaired2_output_file_name

For PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file.

fastp_read1_adapter_sequence

the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.

GATCGGAAGAGC

fastp_read2_adapter_sequence

Argument Name

Summary

Default Value

bwa_mem_Y

Force soft-clipping rather than default hard-clipping of supplementary alignments

True

bwa_mem_T

Don’t output alignment with score lower than INT. This option only affects output.

30

bwa_mem_P

In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.

UBG_bwa_mem_output

Argument Name

Summary

Default Value

UBG_picard_addRG_output_file_name

Output BAM file name for uncollapsed bam generation (Required)

BC_picard_addRG_output_file_name

Output BAM file name for bam collapsing (Required)

picard_addRG_sort_order

Sort order for the BAM file

queryname

Argument Name

Summary

Default Value

UBG_gatk_merge_bam_alignment_output_file_name

Output BAM file name for uncollapsed bam generation (Required)

BC_gatk_merge_bam_alignment_output_file_name

Output BAM file name for bam collapsing (Required)

Argument Name

Summary

Default Value

optical_duplicate_pixel_distance

The maximum offset between two duplicate clusters in order to consider them optical duplicates. The default is appropriate for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is more appropriate. For other platforms and models, users should experiment to find what works best.

2500

read_name_regex

Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.

duplicate_scoring_strategy

The scoring strategy for choosing the non-duplicate among candidates.

gatk_mark_duplicates_output_file_name

Argument Name

Summary

Default Value

bedtools_genomecov_option_bedgraph

option flag parameter to choose output file format. -bg refers to bedgraph format

True

Argument Name

Summary

Default Value

bedtools_merge_distance_between_features

Maximum distance between features allowed for features to be merged.

10

Argument Name

Summary

Default Value

abra2_window_size

Processing window size and overlap (size,overlap)

"400,200"

abra2_soft_clip_contig

Soft clip contig args [maxcontigs,min_base_qual,frac high_qual_bases,min_soft_clip_len]

"16,13,80,15"

abra2_scoring_gap_alignments

Scoring used for contig alignments(match, mismatch_penalty,gap_open_penalty,gap_extend_penalty)

"8,32,48,1"

abra2_no_sort

Argument Name

Summary

Default Value

UBG_picard_fixmateinformation_output_file_name

The output BAM file to write to for uncollapsed bam generation (Required)

BC_picard_fixmate_information_output_file_name

The output BAM file to write to for bam collapsing (Required)

Argument Name

Default Value

gatk_base_recalibrator_known_sites

gatk_bqsr_read_filter

base_recalibrator_output_file_name

Argument Name

Default Value

apply_bqsr_output_file_name

gatk_bqsr_disable_read_filter

Argument Name

Summary

Default Value

fgbio_group_reads_by_umi_input

The input BAM file

fgbio_group_reads_by_umi_strategy

The UMI assignment strategy. (identity, edit, adjacency, paired)

paired

fgbio_group_reads_by_umi_raw_tag

The tag containing the raw UMI.

RX

fgbio_group_reads_by_umi_output_file_name

Argument Name

Summary

Default Value

fgbio_collect_duplex_seq_metrics_intervals

Optional set of intervals over which to restrict analysis.

fgbio_collect_duplex_seq_metrics_output_prefix

Prefix of output files to write.

fgbio_collect_duplex_seq_metrics_min_ba_reads

Minimum BA reads to call a tag family a ‘duplex’.

fgbio_collect_duplex_seq_metrics_min_ab_reads

Argument Name

Summary

Default Value

fgbio_call_duplex_consensus_reads_trim

If true, quality trim input reads in addition to masking low Q bases.

fgbio_call_duplex_consensus_reads_sort_order

The sort order of the output, if :none: then the same as the input.

fgbio_call_duplex_consensus_reads_read_name_prefix

The prefix all consensus read names

fgbio_call_duplex_consensus_reads_read_group_id

Argument Name

Summary

Default Value

fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex

Reverse [complement] per base tags on reverse strand reads.- Simplex+Duplex

fgbio_filter_consensus_read_reverse_per_base_tags_duplex

Reverse [complement] per base tags on reverse strand reads. - Duplex

fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex

Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).

fgbio_filter_consensus_read_require_single_strand_agreement_duplex

Argument Name

Summary

Default Value

fgbio_postprocessing_output_file_name_simplex

Output BAM file name Simplex (Required)

Argument Name

Summary

Default Value

gatk_collect_alignment_summary_metrics_output_file_name

Output file name for metrics on collapsed BAM (Duplex+Simplex+Singletons)

Read group ID to use in the file header (Required)

Read structures, one for each of the FASTQs. Refer to the for more details

Read1 fastq.gz output file name for bam collapsing (Required)

The adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as (string)

Output SAM file name for uncollapsed bam generation (Required)

The output file to write marked records to (Required)

Do not attempt to sort final output

The output BAM file name (Required)

Minimum AB reads to call a tag family a ‘duplex’.

The new read group ID for all the consensus reads.

Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).

0.7.17

4.1.8.1

4.1.8.0

4.1.8.1

2.28.0_cv2

2.28.0_cv2

2.22

4.1.8.1

4.1.8.1

4.1.8.1

1.2.0

1.2.0

1.2.0

1.2.0

0.1.8

4.1.8.0