Description
Views and converts SAM/BAM/CRAM files.
Type
bash_script
License
MIT/Expat
Keywords
Contributors
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bam"
min_MQ: [ 0 ]
min_qlen: [ 0 ]
subsample_seed: [ 0 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.3.1 \
-main-script target/nextflow/samtools/samtools_view/main.nf \
-params-file params.yaml Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input SAM, BAM, or CRAM file. |
--fai_reference -t | file | A tab-delimited FILE. Each line must contain the reference name in the first column and the length of the reference in the second column, with one line for each distinct reference. Any additional fields beyond the second column are ignored. This file also defines the order of the reference sequences in sorting. If you run: `samtools faidx <ref.fa>', the resulting index file <ref.fa>.fai can be used as this FILE. |
--reference -T | file | A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools faidx. If an index is not present one will be generated for you, if the reference file is local. If the reference file is not local, but is accessed instead via an https://, s3:// or other URL, the index file will need to be supplied by the server alongside the reference. It is possible to have the reference and index files in different locations by supplying both to this option separated by the string "##idx##", for example: --reference ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai However, note that only the location of the reference will be stored in the output file header. If this method is used to make CRAM files, the cram reader may not be able to find the index, and may not be able to decode the file unless it can get the references it needs using a different method. |
--target_file -L | file | Only output alignments overlapping the input BED FILE [null]. |
--region_file | file | Use an index and multi-region iterator to only output alignments overlapping the input BED FILE. Equivalent to --use_index --target_file FILE. |
--qname_file -N | file | Output only alignments with read names listed in FILE. If FILE starts with ^ then the operation is negated and only outputs alignment with read groups not listed in FILE. It is not permissible to mix both the filter-in and filter-out style syntax in the same command. |
--read_group_file -R | file | Output alignments in read groups listed in FILE [null]. If FILE starts with ^ then the operation is negated and only outputs alignment with read names not listed in FILE. It is not permissible to mix both the filter-in and filter-out style syntax in the same command. Note that records with no RG tag will also be output when using this option. This behaviour may change in a future release. |
--use_index -M | boolean_true | Use the multi-region iterator on the union of a BED file and command-line region arguments. This avoids re-reading the same regions of files so can sometimes be much faster. Note this also removes duplicate sequences. Without this a sequence that overlaps multiple regions specified on the command line will be reported multiple times. The usage of a BED file is optional and its path has to be preceded by --target_file option. |
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output to FILE instead of [stdout]. |
--bam -b | boolean_true | Output in the BAM format. |
--cram -C | boolean_true | Output in the CRAM format (requires --reference). |
--fast | boolean_true | Enable fast compression. This also changes the default output format to BAM, but this can be overridden by the explicit format options or using a filename with a known suffix. |
--uncompressed -u | boolean_true | Output uncompressed data. This also changes the default output format to BAM, but this can be overridden by the explicit format options or using a filename with a known suffix. This option saves time spent on compression/decompression and is thus preferred when the output is piped to another samtools command. |
--with_header | boolean_true | Include the header in the output. |
--header_only -H | boolean_true | Output the header only. |
--no_header | boolean_true | When producing SAM format, output alignment records but not headers. This is the default; the option can be used to reset the effect of --with_header/--header_only. |
--count -c | boolean_true | Instead of printing the alignments, only count them and print the total number. All filter options, such as --require_flags, --excl_flags, and --min_MQ, are taken into account. The --unmap option is ignored in this mode. |
--output_unselected -U | file | Write alignments that are not selected by the various filter options to FILE. When this option is used, all alignments (or all alignments intersecting the regions specified) are written to either the output file or this file, but never both. |
--unmap -p | boolean_true | Set the UNMAP flag on alignments that are not selected by the filter options. These alignments are then written to the normal output. This is not compatible with --output_unselected. |
--read_group -r | string | Output alignments in read group STR [null]. Note that records with no RG tag will also be output when using this option. This behaviour may change in a future release. |
--tag -d | string | Only output alignments with tag STR1 and associated value STR2, which can be a string or an integer [null]. The value can be omitted, in which case only the tag is considered. Note that this option does not specify a tag type. For example, use --tag XX:42 to select alignments with an XX:i:42 field, not --tag XX:i:42. |
--tag_file -D | file | Only output alignments with tag STR and associated values listed in FILE. |
--min_MQ -q | integer | Skip alignments with MAPQ smaller than INT. |
--library -l | string | Only output alignments in library STR. |
--min_qlen -m | integer | Only output alignments with number of CIGAR bases consuming query sequence >= INT. |
--expr -e | string | Only include alignments that match the filter expression STR. The syntax for these expressions is described in the main samtools. |
--require_flags -f | string | Only output alignments with all bits set in FLAG present in the FLAG field. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. |
--excl_flags -F | string | Do not output alignments with any bits set in FLAG present in the FLAG field. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. |
--excl_all_flags -G | integer | Do not output alignments with all bits set in INT present in the FLAG field. This is the opposite of --require_flags such that --require_flags 12 --exclude_all_flags 12 is the same as no filtering at all. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. |
--incl_flags --rf | string | Only output alignments with any bit set in FLAG present in the FLAG field. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. |
--remove_tag -x | string | Read tag(s) to exclude from output (repeatable) [null]. This can be a single tag or a comma separated list. Alternatively the option itself can be repeated multiple times. If the list starts with a `^' then it is negated and treated as a request to remove all tags except those in STR. The list may be empty, so --remove_tag ^ will remove all tags. Note that tags will only be removed from reads that pass filtering. |
--keep_tag | string | This keeps only tags listed in STR and is directly equivalent to --remove_tag ^STR. Specifying an empty list will remove all tags. If both --keep_tag and --remove_tag are specified then --keep_tag has precedence. Note that tags will only be removed from reads that pass filtering. |
--remove_B -B | boolean_true | Collapse the backward CIGAR operation. |
--add_flags | string | Adds flag(s) to read. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names. |
--remove_flags | string | Remove flag(s) from read. FLAG is specified in the same way as with the --add_flags option. |
--subsample | double | Output only a proportion of the input alignments, as specified by 0.0 <= FLOAT <= 1.0, which gives the fraction of templates/pairs to be kept. This subsampling acts in the same way on all of the alignment records in the same template or read pair, so it never keeps a read but not its mate. |
--subsample_seed | integer | Subsampling seed used to influence which subset of reads is kept. When subsampling data that has previously been subsampled, be sure to use a different seed value from those used previously; otherwise more reads will be retained than expected. |
--fetch_pairs -P | boolean_true | Retrieve pairs even when the mate is outside of the requested region. Enabling this option also turns on the multi-region iterator (-M). A region to search must be specified, either on the command-line, or using the --target_file option. The input file must be an indexed regular file. This option first scans the requested region, using the RNEXT and PNEXT fields of the records that have the PAIRED flag set and pass other filtering options to find where paired reads are located. These locations are used to build an expanded region list, and a set of QNAMEs to allow from the new regions. It will then make a second pass, collecting all reads from the originally-specified region list together with reads from additional locations that match the allowed set of QNAMEs. Any other filtering options used will be applied to all reads found during this second pass. As this option links reads using RNEXT and PNEXT, it is important that these fields are set accurately. Use 'samtools fixmate' to correct them if necessary. Note that this option does not work with the --count, --output-unselected or --unmap options. |
--customized_index -X | boolean_true | Include customized index file as a part of arguments. See EXAMPLES section for sample of usage. |
--sanitize -z | string | Perform some sanity checks on the state of SAM record fields, fixing up common mistakes made by aligners. These include soft-clipping alignments when they extend beyond the end of the reference, marking records as unmapped when they have reference * or position 0, and ensuring unmapped alignments have no CIGAR or mapping quality for unmapped alignments and no MD, NM, CG or SM tags. FLAGs is a comma-separated list of keywords chosen from the following list. unmap: The UNMAPPED BAM flag. This is set for reads with position <= 0, reference name "*" or reads starting beyond the end of the reference. Note CIGAR "*" is permitted for mapped data so does not trigger this. pos: Position and reference name fields. These may be cleared when a sequence is unmapped due to the coordinates being beyond the end of the reference. Selecting this may change the sort order of the file, so it is not a part of the on compound argument. mqual: Mapping quality. This is set to zero for unmapped reads. cigar: Modifies CIGAR fields, either by adding soft-clips for reads that overlap the end of the reference or by clearing it for unmapped reads. aux: For unmapped data, some auxiliary fields are meaningless and will be removed. These include NM, MD, CG and SM. off: Perform no sanity fixing. This is the default on: Sanitize data in a way that guarantees the same sort order. This is everything except for pos. all: All sanitizing options, including pos. |
--no_PG | boolean_true | Do not add a @PG line to the header of the output file. |
--input_fmt_option | string | Specify a single input file format option in the form of OPTION or OPTION=VALUE. |
--output_fmt -O | string | Specify output format (SAM, BAM, CRAM). |
--output_fmt_option | string | Specify a single output file format option in the form of OPTION or OPTION=VALUE. |
--write_index | boolean_true | Automatically index the output files. |