Official announcement:

Samtools Release 1.5 [Solstice Release] (21st June 2017)

• Samtools fastq now has a -i option to create a fastq file from an index tag, and a -T option (similar to -t) to add user specified aux tags to the fastq header line.
• Samtools fastq can now create compressed fastq files, by giving the output filenames an extention of .gq, .bgz, or .bgzf
• Samtools sort has a -t TAG option, that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged.

Let's go over each item and see how it works in practice.

Samtools fastq now has a -i option to create a fastq file from an index tag, and a -T option (similar to -t) to add user specified aux tags to the fastq header line.

Help flags for samtools fastq:

...
    -i          add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)
    -T TAGLIST  copy arbitrary tags to the FASTQ header line
...

Let's give it a go. Get the test file.

curl https://raw.githubusercontent.com/samtools/samtools/develop/test/dat/bam2fq.005.sam > test.sam

now run:

samtools fastq test.sam | head -4

it prints

@ref1_grp1_p001/1
CGAGCTCGGT
+
!!!!!!!!!!

whereas:

samtools fastq -T MD,BC,za test.sam | head -4

prints:

@ref1_grp1_p001/1   MD:Z:10 BC:Z:AC-GT  za:Z:Hello world!
CGAGCTCGGT
+
!!!!!!!!!!

The -i flag is poorly documented and I managed to figure it out only by scouring the test examples on the GitHub repository. It requires setting the --index-format parameter and a file specified via the --i1 parameter to collect the indices into.

samtools fastq -i --i1 indices.fq --index-format 'i2' -T MD,BC,za test.sam | head -4

will produce:

@ref1_grp1_p001/1   MD:Z:10 BC:Z:AC-GT  za:Z:Hello world! 1:N:0:AC
CGAGCTCGGT
+
!!!!!!!!!!

and a file called indices.fq that contains:

@ref1_grp1_p001/1   MD:Z:10 BC:Z:AC-GT  za:Z:Hello world! 1:N:0:AC
AC
+
""
@ref1_grp1_p002/1   MD:Z:10 BC:Z:AATT+CCGG  za:Z:Another string 1:N:0:AA
AA
+
""
@ref1_grp2_p001/1   MD:Z:8  BC:Z:TG+CA  za:Z:!"$%^&*() 1:N:0:TG
TG
+
ab

Samtools fastq can now create compressed fastq files, by giving the output filenames an extention of .gq, .bgz, or .bgzf

Example:

samtools fastq -1 read1.fq.gz -2 read2.fq.gz align.bam

The release note is a bit confusing though.It is not clear what the .qg extension above means.Perhaps a typo for .gz since that works as well as demonstrated above. Also unclear is the difference between .bgz and bgzf.

Samtools sort has a -t TAG option, that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged.

samtools sort align.bam | samtools view | cut -f 1,12-25 | head -5

prints:

SRR343051.887   NM:i:0  MD:Z:101    AS:i:101    XS:i:101    RG:Z:foo    XA:Z:NC_020370.1,-55728,101M,0;
SRR343051.542   NM:i:0  MD:Z:101    AS:i:101    XS:i:101    RG:Z:foo    XA:Z:NC_020370.1,-55615,101M,0;
SRR343051.9863  NM:i:0  MD:Z:101    AS:i:101    XS:i:101    RG:Z:foo    XA:Z:NC_020370.1,-55587,101M,0;
SRR343051.887   NM:i:0  MD:Z:101    AS:i:101    XS:i:101    RG:Z:foo    XA:Z:NC_020370.1,+55573,101M,0;
SRR343051.9863  NM:i:0  MD:Z:101    AS:i:101    XS:i:101    RG:Z:foo    XA:Z:NC_020370.1,+55479,101M,0;

whereas:

samtools sort -t AS align.bam | samtools view | cut -f 1,12-25 | head -5

prints:

SRR343051.1909  AS:i:0  XS:i:0  RG:Z:foo
SRR343051.5040  AS:i:0  XS:i:0  RG:Z:foo
SRR343051.22    AS:i:0  XS:i:0  RG:Z:foo
SRR343051.2588  AS:i:0  XS:i:0  RG:Z:foo
SRR343051.3324  AS:i:0  XS:i:0  RG:Z:foo