I have a bam file sample.bam. I would like to create a smaller version for testing my pipeline. I tried this:

samtools view sample.bam > temp.sam
head -1000000 temp.sam > temp1e6.sam
samtools -bT temp1e6.sam > short.bam

Now short.bam looks like:

$ cat short.bam

Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options:
  -b       output BAM
  -C       output CRAM (requires -T)
  -1       use fast BAM compression (implies -b)
  -u       uncompressed BAM output (implies -b)
  -h       include header in SAM output
  -H       print SAM header only (no alignments)
  -c       print only the count of matching records
  -o FILE  output file name [stdout]
  -U FILE  output reads not selected by filters to FILE [null]
  -t FILE  FILE listing reference names and lengths (see long help) [null]
  -L FILE  only include reads overlapping this BED FILE [null]
  -r STR   only include reads in read group STR [null]
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