Hi @Pierre Lindenbaum,

Thanks for the feedback. However, for some reason running the --input-fmt-option CRAM causes the following error

[E::hts_opt_add] Unknown option 'CRAM'
Usage: samtools merge [-nurlf] [-h inh.sam] [-b <bamlist.fofn>] <out.bam> <in1.bam> [<in2.bam> ... <inN.bam>]

Options:
  -n         Input files are sorted by read name
  -t TAG     Input files are sorted by TAG value
  -r         Attach RG tag (inferred from file names)
  -u         Uncompressed BAM output
  -f         Overwrite the output BAM if exist
  -1         Compress level 1
  -l INT     Compression level, from 0 to 9 [-1]
  -R STR     Merge file in the specified region STR [all]
  -h FILE    Copy the header in FILE to <out.bam> [in1.bam]
  -c         Combine @RG headers with colliding IDs [alter IDs to be distinct]
  -p         Combine @PG headers with colliding IDs [alter IDs to be distinct]
  -s VALUE   Override random seed
  -b FILE    List of input BAM filenames, one per line [null]
  -X         Use customized index files
  -L FILE    Specify a BED file for multiple region filtering [null]
  --no-PG    do not add a PG line
      --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]
  -@, --threads INT
               Number of additional threads to use [0]
      --write-index
               Automatically index the output files [off]
      --verbosity INT
               Set level of verbosity

Any idea why?