BamToFastq.md

BamToFastq tool help

BamToFastq (2023_03-63-gec44de43)

Converts a coordinate-sorted BAM file to FASTQ files.

Mandatory parameters:
  -in <file>               Input BAM/CRAM file.
  -out1 <file>             Read 1 output FASTQ.GZ file.

Optional parameters:
  -out2 <file>             Read 2 output FASTQ.GZ file (required for pair-end samples).
                           Default value: ''
  -mode <enum>             Determine if BAM/CRAM contains paired-end or single-end reads (default: paired-end)
                           Default value: 'paired-end'
                           Valid: 'paired-end,single-end'
  -reg <string>            Export only reads in the given region. Format: chr:start-end.
                           Default value: ''
  -remove_duplicates       Does not export duplicate reads into the FASTQ file.
                           Default value: 'false'
  -compression_level <int> Output FASTQ compression level from 1 (fastest) to 9 (best compression).
                           Default value: '1'
  -write_buffer_size <int> Output write buffer size (number of FASTQ entry pairs).
                           Default value: '100'
  -ref <file>              Reference genome for CRAM support (mandatory if CRAM is used).
                           Default value: ''

Special parameters:
  --help                   Shows this help and exits.
  --version                Prints version and exits.
  --changelog              Prints changeloge and exits.
  --tdx                    Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

BamToFastq changelog

BamToFastq 2023_03-63-gec44de43

2023-03-22 Added mode for single-end samples (long reads).
2020-11-27 Added CRAM support.
2020-05-29 Massive speed-up by writing in background. Added 'compression_level' parameter.
2020-03-21 Added 'reg' parameter.

back to ngs-bits