Detailed Usage

Marianas Sub-commands and Parameters

Note: All parameters are positional, and are listed in the following tables in the order they should be supplied. Also note that the defaults listed here are the recommended values from our testing, however they are not internal to the tool, and still must be supplied on the command line.

Bam Collapsing

ProcessLoopUMIFastq

Parameter	Description	Default
read_1	Path to read 1 of paired fastqs
read_2	Path to read 2 of paired fastqs
umi_length	Number of bases that constitute the UMI for each read	3

DuplexUMIBamToCollapsedFastqFirstPass & DuplexUMIBamToCollapsedFastqSecondPass

Parameter	Description	Default
bam_file	Path to .bam file after it has been run through ProcessLoopUMIFastq and the standard Picard and GATK pipeline
pileup_file	(optional) Path to a pileup file generated by Waltz for the current sample being processed. If provided, the genotype at each position from this file will be used to decide the consensus base to use if min_consensus_percent is not reached.
min_mapq	Minimum mapping quality	1
min_basq	Minimum base quality	20
umi_mismatches	UMI families with less than or equal to this many mismatches that map at the same position (within umi_wobble distance) will be merged and collapsed as one family	0
umi_wobble	UMI families that map to within this many bases as each other will be merged and collapsed as one family (if they also satisfy requirement for umi_mismatches)	2
min_consensus_percent	Positions with a single base that is represented in greater than or equal to this many reads will be collapsed with the corresponding consensus base. If no consensus can be reached this position will be output as an N.	90
reference_fasta	Path to reference fasta which will be used as a backup to decide a consensus base if no pileup file is provided.	HG19
minInsertionConsensusPercent [internal]	Similar to min_consensus_percent, this threshold will be used to decide on whether to include insertions in the collapsed consensus sequence.	70
minDeletionConsensusPercent [internal]	Similar to min_consensus_percent, this threshold will be used to decide on whether to include deletions in the collapsed consensus sequence.	50
basesToTrim [internal]	Number of bases to trim from either end of the consensus sequences after collapsing	3

SeparateBams

Parameter	Description
bam_file	Collapsed bam file that should be split into two bams consisting of only Simplex and Duplex reads

Polishing

NoiseFrequencyBuilder

Parameter	Description
pileup_directory	Directory that contains Waltz pileups for a set of normal bam files

Polisher

Parameter	Description
maf_file	These columns are required: Chromosome, Start_Position, Variant_Type, Reference_Allele, Tumor_Seq_Allele2
depth_column_name	Column name for MAF field that represents sequencing depth
alt_count_column_name	Column name for MAF field that represents alt allele count
af_frequencies_file	af-frequencies.txt from NoiseFrequencyBuilder
count_frequencies_file	count-frequencies.txt from NoiseFrequencyBuilder