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samtools-reference(1) Bioinformatics tools samtools-reference(1) NAME samtools reference - extracts an embedded reference from a CRAM file SYNOPSIS samtools reference [-q] [-r region] [-o out.fa] in.cram DESCRIPTION Creates the reference from aligned data using either the MD:Z auxiliary tags or an embedded reference in a CRAM file. The output is a FASTA file. For the embedded reference mode (-e) this operation is fast, but only works on CRAMs produced using --output-fmt-option embed_ref=1. Note this may not be the complete reference used. Each CRAM slice will hold the entire ref- erence that spans the slice coordinates, but gaps in coverage can lead to gaps between slices. However this reference should be suitable for passing into a CRAM decode (samtools view -T ref.fa). For SAM/BAM files or CRAMs without reference, using the MD:Z tag may also produce an incomplete reference. Unlike embedded reference, this reference may not be sufficient for decoding a CRAM file as the CRAM slice headers store the MD5sum of the portion of reference than spans that slice, but the slice may not have 100% coverage leading to Ns in the computed reference. However it should still be possible to decode such CRAMs by ignoring the md5 mismatches using e.g. samtools view --input-fmt-option ignore_md5=1. OPTIONS -e Enable CRAM embedded reference mode. -q Enables quiet mode and will produce no output. By default a line per reference is reporting describing the percentage with non-N bases. -r region Specifies a single region to produce the reference from. If speci- fied, an index file must be present. -o FILE Write the FASTA records to FILE. By default this is sent to std- out. -@ INT The number of BAM/CRAM decompression threads to use in addition to the main thread [0]. Note this does not multi-thread the main reference generation steps, so scaling may be capped by 2 or 3 threads, depending on the data. It will also not affect the -e option for CRAM embedded ref- erence, although this is already the fastest method. AUTHOR Written by James Bonfield from the Sanger Institute. SEE ALSO samtools(1) Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-reference(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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