Some clarification about sam to bam conversion

[finswimmer]

Hello,
for getting a sorted bam file out of an unsorted sam file i often found these commands:

samtools view -bS file.sam | samtools sort - > file_sorted.bam
samtools view -bT reference.fa file.sam | samtools sort - > file_sorted.bam

My questions are:
1. When do I need to give the reference file as an argument?
2. Are there any disadvantages if I do this:

samtools sort -O BAM file.sam > file_sorted.bam

fin swimmer

[dpryan]

1. You only need to do that with CRAM files (and usually not even then)
2. Samtools sort doesn't accept BAM input.

As an aside, you can use the following for a slight speed improvement:

samtools view -uS file.sam | samtools sort - > file_sorted.bam

Note that the syntax for "samtools sort" has changed in more recent versions.

[finswimmer]

Hello

1. You only need to do that with CRAM files (and usually not even then)
2. Samtools sort doesn't accept BAM input.

you mean doesn't accept SAM input?

samtools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.

Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]

The strange thing is, that I didn't see any problems until now by sorting the way I described above...

fin swimmer

[dpryan]

Oops, yes I meant SAM input. That at least used to not work, but perhaps it's been silently changed.