List bams with missing indices / index

list_bams_missing_index.sh

function check_file {
  if [ ! -s "$1" ]
    then
     	echo "$1 not found"
  fi
}
export -f check_file

# List bams with a missing bai index
ls -1 *.bam | parallel check_file {}.bai
# List bai's with a missing bam
ls -1 *.bai | sed 's/.bai//' | parallel check_file {}