Shell script that takes a reference and a SAM file (both should be small) converts sam to sorted BAM and displays ist using `samtools tview`.

quick_view.sh

#!/bin/bash

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
FIX=$DIR/fix_sam.py

# Global variables for reference REF and SAM alignment.
REF=
SAM=
# Whether or not verbose mode is enabled.
VERBOSE=
# Whether or not to keep the files.
KEEP=
# Temporary directory created.
TMPDIR=$(mktemp -d)

# Remove temporary directory at exit/crashes.
function cleanup {
    test -z "$KEEP" || return
    test -z "$VERBOSE" || echo "rm -rf ${TMPDIR}" >&2
    rm -rf ${TMPDIR}
}

trap cleanup EXIT

# Parse parameters.

while getopts "r:s:vk" opt; do
    case $opt in
        r)
            REF=$OPTARG
            ;;
        s)
            SAM=$OPTARG
            ;;
        v)
            VERBOSE=1
            ;;
        k)
            KEEP=1
            ;;
        \?)
            echo "Invalid option: -$OPTARG" >&2
            exit 1
            ;;
  esac
done

# Check parameters.

if [[ -z "$REF" ]]; then
    echo "Parameter -r required" >&2
    exit 1
fi

if [[ -z "$SAM" ]]; then
    echo "Parameter -s required" >&2
    exit 1
fi

# Copy reference into temp dir.
test -z "$VERBOSE" || echo "cp $REF $TMPDIR"/ref.fa >&2
cp $REF $TMPDIR/ref.fa

# Strip leading 1I from CIGAR strings.
test -z "$VERBOSE" || echo "$FIX <$SAM >$TMPDIR/aln.sam"
$FIX <$SAM >$TMPDIR/aln.sam

# Convert SAM file to BAM file and sort it.
test -z "$VERBOSE" || echo "samtools view -Sb $TMPDIR/aln.sam > $TMPDIR/aln.bam" >&2
samtools view -Sb $TMPDIR/aln.sam > $TMPDIR/aln.bam

Also see https://gist.github.com/holtgrewe/8735840.