'\" t .TH samtools-import 1 "24 January 2024" "samtools-1.19.2" "Bioinformatics tools" .SH NAME samtools-import \- converts FASTQ files to unmapped SAM/BAM/CRAM .\" .\" Copyright (C) 2020 Genome Research Ltd. .\" .\" Author: James Bonfield .\" .\" Permission is hereby granted, free of charge, to any person obtaining a .\" copy of this software and associated documentation files (the "Software"), .\" to deal in the Software without restriction, including without limitation .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, .\" and/or sell copies of the Software, and to permit persons to whom the .\" Software is furnished to do so, subject to the following conditions: .\" .\" The above copyright notice and this permission notice shall be included in .\" all copies or substantial portions of the Software. .\" .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER .\" DEALINGS IN THE SOFTWARE. . .\" For code blocks and examples (cf groff's Ultrix-specific man macros) .de EX . in +\\$1 . nf . ft CR .. .de EE . ft . fi . in .. . .SH SYNOPSIS .PP samtools import .RI [ options ] [ .I fastq_file \fR... ] .SH DESCRIPTION .PP 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 \fB-1\fR and \fB-2\fR for READ1 and READ2 data files, \fB-s\fR for an interleaved paired file (or one half of a paired-end run), \fB-0\fR for unpaired data and explicit index files specified with \fB--i1\fR and \fB--i2\fR. These correspond to typical output produced by Illumina bcl2fastq and match the output from \fBsamtools fastq\fR. The index files will set both the \fBBC\fR barcode code and it's associated \fBQT\fR quality tag. The Illumina CASAVA identifiers may also be processed when the \fB-i\fR 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 \fBBC\fR 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. .SH OPTIONS .TP 8 .BI -s\ FILE Import paired interleaved data from \fIFILE\fR. .TP 8 .BI -0\ FILE Import single-ended (unpaired) data from \fIFILE\fR. Operationally there is no difference between the \fB-s\fR and \fB-0\fR 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. .TP 8 .BI -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. .TP 8 .BI --i1\ FILE ,\ --i2\ FILE Specifies index barcodes associated with the \fB-1\fR and \fB-2\fR files. These will be appended to READ1 and READ2 records in the barcode (BC) and quality (QT) tags. .TP 8 .B -i Specifies that the Illumina CASAVA identifiers should be processed. This may set the READ1, READ2 and QCFAIL flags and add a barcode tag. .TP .B -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. .TP .BI --barcode-tag\ TAG Changes the auxiliary tag used for barcode sequence. Defaults to BC. .TP .BI --quality-tag\ TAG Changes the auxiliary tag used for barcode quality. Defaults to QT. .TP .BI -o FILE Output to \fIFILE\fR. By default output will be written to stdout. .TP 8 .BI --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 \fBsamtools sort -t TAG\fR 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. \fB--order rn:12\fR will be able to sort up to 1 trillion records. .TP 8 .BI -r\ RG_line ,\ --rg-line\ RG_line A complete \fB@RG\fR header line may be specified, with or without the initial "@RG" component. If specified this will also use the ID field from \fIRG_line\fR in each SAM records RG auxiliary tag. If specified multiple times this appends to the RG line, automatically adding tabs between invocations. .TP 8 .BI -R\ RG_ID ,\ --rg\ RG_ID This is a shorter form of the option above, equivalent to \fB--rg-line ID:\fR\fIRG_ID\fR. If both are specified then this option is ignored. .TP .B -u Output BAM or CRAM as uncompressed data. .TP 8 .BI -T\ TAGLIST This looks for any SAM-format auxiliary tags in the comment field of a fastq read name. These must match the :: pattern as specified in the SAM specification. \fITAGLIST\fR can be blank or \fB*\fR 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. .SH EXAMPLES Convert a single-ended fastq file to an unmapped CRAM. Both of these commands perform the same action. .EX 4 samtools import -0 in.fastq -o out.cram samtools import in.fastq > out.cram .EE Convert a pair of Illumina fastqs containing CASAVA identifiers to BAM, adding the barcode information to the BC auxiliary tag. .EX 4 samtools import -i -1 in_1.fastq -2 in_2.fastq -o out.bam samtools import -i in_[12].fastq > out.bam .EE Specify the read group. These commands are equivalent .EX 4 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 .EE 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. .EX 4 samtools import -i -1 R1.fq -2 R2.fq --i1 I1.fq --i2 I2.fq -o out.bam .EE 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. .EX 4 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*" .EE .SH AUTHOR .PP Written by James Bonfield of the Wellcome Sanger Institute. .SH SEE ALSO .IR samtools (1), .IR samtools-fastq (1) .PP Samtools website: