NAME

samtools import - converts FASTQ files to unmapped SAM/BAM/CRAM

SYNOPSIS

samtools import [options] [ fastq_file ... ]

DESCRIPTION

Reads one or more FASTQ files and converts them to unmapped SAM, BAM or CRAM. The input files may be automatically decompressed if they have a .gz extension.

The simplest usage in the absence of any other command line options is to provide one or two input files.

If a single file is given, it will be interpreted as a single-ended sequencing format unless the read names end with /1 and /2 in which case they will be labelled as PAIRED with READ1 or READ2 BAM flags set. If a pair of filenames are given they will be read from alternately to produce an interleaved output file, also setting PAIRED and READ1 / READ2 flags.

The filenames may be explicitly labelled using -1 and -2 for READ1 and READ2 data files, -s for an interleaved paired file (or one half of a paired-end run), -0 for unpaired data and explicit index files specified with --i1 and --i2. These correspond to typical output produced by Illumina bcl2fastq and match the output from samtools fastq. The index files will set both the BC barcode code and it's associated QT quality tag.

The Illumina CASAVA identifiers may also be processed when the -i option is given. This tag will be processed for READ1 / READ2, whether or not the read failed processing (QCFAIL flag), and the barcode sequence which will be added to the BC tag. This can be an alternative to explicitly specifying the index files, although note that doing so will not fill out the barcode quality tag.

OPTIONS

-s FILE

Import paired interleaved data from FILE.

-0 FILE

Import single-ended (unpaired) data from FILE.

Operationally there is no difference between the -s and -0 options as given an interleaved file with /1 and /2 read name endings both will correctly set the PAIRED, READ1 and READ2 flags, and given data with no suffixes and no CASAVA identifiers being processed both will leave the data as unpaired. However their inclusion here is for more descriptive command lines and to improve the header comment describing the samtools fastq decode command.

-1 FILE, -2 FILE

Import paired data from a pair of FILEs. The BAM flag PAIRED will be set, but not PROPER_PAIR as it has not been aligned. READ1 and READ2 will be stored in their original, unmapped, orientation.

--i1 FILE, --i2 FILE

Specifies index barcodes associated with the -1 and -2 files. These will be appended to READ1 and READ2 records in the barcode (BC) and quality (QT) tags.

-i

Specifies that the Illumina CASAVA identifiers should be processed. This may set the READ1, READ2 and QCFAIL flags and add a barcode tag.

-N, --name2

Assume the read names are encoded in the SRA and ENA formats where the first word is an automatically generated name with the second field being the original name. This option extracts that second field instead.

--barcode-tag TAG

Changes the auxiliary tag used for barcode sequence. Defaults to BC.

--quality-tag TAG

Changes the auxiliary tag used for barcode quality. Defaults to QT.

-oFILE

Output to FILE. By default output will be written to stdout.

--order TAG

When outputting a SAM record, also output an integer tag containing the Nth record number. This may be useful if the data is to be sorted or collated in some manner and we wish this to be reversible. In this case the tag may be used with samtools sort -t TAG to regenerate the original input order.

Note integer tags can only hold up to 2^32 record numbers (approximately 4 billion). Data sets with more records can switch to using a fixed-width string tag instead, with leading 0s to ensure sort works. To do this specify TAG:LENGTH. E.g. --order rn:12 will be able to sort up to 1 trillion records.

-r RG_line, --rg-line RG_line

A complete @RG header line may be specified, with or without the initial "@RG" component. If specified this will also use the ID field from RG_line in each SAM records RG auxiliary tag.

If specified multiple times this appends to the RG line, automatically adding tabs between invocations.

-R RG_ID, --rg RG_ID

This is a shorter form of the option above, equivalent to --rg-line ID:RG_ID. If both are specified then this option is ignored.

-u

Output BAM or CRAM as uncompressed data.

-T TAGLIST

This looks for any SAM-format auxiliary tags in the comment field of a fastq read name. These must match the <alpha-num><alpha-num>:<type>:<data> pattern as specified in the SAM specification. TAGLIST can be blank or * to indicate all tags should be copied to the output, otherwise it is a comma-separated list of tag types to include with all others being discarded.

EXAMPLES

Convert a single-ended fastq file to an unmapped CRAM. Both of these commands perform the same action.

samtools import -0 in.fastq -o out.cram
samtools import in.fastq > out.cram

Convert a pair of Illumina fastqs containing CASAVA identifiers to BAM, adding the barcode information to the BC auxiliary tag.

samtools import -i -1 in_1.fastq -2 in_2.fastq -o out.bam
samtools import -i in_[12].fastq > out.bam

Specify the read group. These commands are equivalent

samtools import -r "$(echo -e 'ID:xyz\tPL:ILLUMINA')" in.fq
samtools import -r "$(echo -e '@RG\tID:xyz\tPL:ILLUMINA')" in.fq
samtools import -r ID:xyz -r PL:ILLUMINA in.fq

Create an unmapped BAM file from a set of 4 Illumina fastqs from bcf2fastq, consisting of two read and two index tags. The CASAVA identifier is used only for setting QC pass / failure status.

samtools import -i -1 R1.fq -2 R2.fq --i1 I1.fq --i2 I2.fq -o out.bam

Convert a pair of CASAVA barcoded fastq files to unmapped CRAM with an incremental record counter, then sort this by minimiser in order to reduce file space. The reversal process is also shown using samtools sort and samtools fastq.

samtools import -i in_1.fq in_2.fq --order ro -O bam,level=0 | \


    samtools sort -@4 -M -o out.srt.cram -
samtools sort -@4 -O bam -u -t ro out.srt.cram | \


    samtools fastq -1 out_1.fq -2 out_2.fq -i --index-format "i*i*"

AUTHOR