samtools-reference - extracts an embedded reference from a CRAM file
samtools reference [
-q] [
-r region] [
-o
out.fa]
in.cram
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 reference 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.
- -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
specified, an index file must be present.
-
-o FILE
- Write the FASTA records to FILE. By default this is
sent to stdout.
-
-@ 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 reference, although
this is already the fastest method.
Written by James Bonfield from the Sanger Institute.
samtools(1)
Samtools website: <
http://www.htslib.org/>