Revert "Don't sort"

This reverts commit b7d9dad9.

bwa.wdl

@@ -110,7 +110,13 @@ task Kit {
         k8 /opt/conda/bin/bwa-postalt.js \
           -p ~{outputPrefix}.hla \
           ~{bwaIndex.fastaFile}~{true=".64.alt" false=".alt" sixtyFour} | \
-        samtools view -b -1 - > ~{outputPrefix}.aln.bam
+        samtools sort \
+          ~{"-@ " + sortThreads} \
+          -m ~{sortMemoryPerThread} \
+          -l ~{compressionLevel} \
+          - \
+          -o ~{outputPrefix}.aln.bam
+        samtools index ~{outputPrefix}.aln.bam ~{outputPrefix}.aln.bai
     }
 
     output {