FastqToBam

Overview

Group: FASTQ

Generates an unmapped BAM (or SAM or CRAM) file from fastq files. Takes in one or more fastq files (optionally gzipped), each representing a different sequencing read (e.g. R1, R2, I1 or I2) and can use a set of read structures to allocate bases in those reads to template reads, sample indices, unique molecular indices, or to designate bases to be skipped over.

Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:

1. T identifies a template read
2. B identifies a sample barcode read
3. M identifies a unique molecular index read
4. S identifies a set of bases that should be skipped or ignored

The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:

--input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B

Alternative if you know your reads are of fixed length you could specify:

--input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B

For more information on read structures see the Read Structure Wiki Page

UMIs may be extracted from the read sequences, the read names, or both. If --extract-umis-from-read-names is specified, any UMIs present in the read names are extracted; read names are expected to be :-separated with any UMIs present in the 8th field. If this option is specified, the --umi-qual-tag option may not be used as qualities are not available for UMIs in the read name. If UMI segments are present in the read structures those will also be extracted. If UMIs are present in both, the final UMIs are constructed by first taking the UMIs from the read names, then adding a hyphen, then the UMIs extracted from the reads.

The same number of input files and read structures must be provided, with one exception: if supplying exactly 1 or 2 fastq files, both of which are solely template reads, no read structures need be provided.

The output file can be sorted by queryname using the --sort-order option; the default is to produce a BAM with reads in the same order as they appear in the fastq file.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToFastq	Fastq files corresponding to each sequencing read (e.g. R1, I1, etc.).	Required	Unlimited
output	o	PathToBam	The output SAM or BAM file to be written.	Required	1
read-structures	r	ReadStructure	Read structures, one for each of the FASTQs.	Optional	Unlimited
sort	s	Boolean	If true, queryname sort the BAM file, otherwise preserve input order.	Optional	1	false
umi-tag	u	String	Tag in which to store molecular barcodes/UMIs.	Optional	1	RX
umi-qual-tag	q	String	Tag in which to store molecular barcode/UMI qualities.	Optional	1
store-sample-barcode-qualities	Q	Boolean	Store the sample barcode qualities in the QT Tag.	Optional	1	false
extract-umis-from-read-names	n	Boolean	Extract UMI(s) from read names and prepend to UMIs from reads.	Optional	1	false
read-group-id		String	Read group ID to use in the file header.	Optional	1	A
sample		String	The name of the sequenced sample.	Required	1
library		String	The name/ID of the sequenced library.	Required	1
barcode	b	String	Library or Sample barcode sequence.	Optional	1
platform		String	Sequencing Platform.	Optional	1	illumina
platform-unit		String	Platform unit (e.g. ‘..')	Optional	1
platform-model		String	Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)	Optional	1
sequencing-center		String	The sequencing center from which the data originated	Optional	1
predicted-insert-size		Integer	Predicted median insert size, to insert into the read group header	Optional	1
description		String	Description of the read group.	Optional	1
comment		String	Comment(s) to include in the output file’s header.	Optional	Unlimited
run-date		Iso8601Date	Date the run was produced, to insert into the read group header	Optional	1