Changes

   bin/bwa samse -r "@RG\tID:ILLUMINA\tSM:SAMPLE1" ref/human_g1k_v37_chr20.fa bwa.sai/SAMPLE1.sai fastq/SAMPLE1.fastq | \

   bin/bwa samse -r "@RG\tID:ILLUMINA\tSM:SAMPLE1" ref/human_g1k_v37_chr20.fa bwa.sai/SAMPLE1.sai fastq/SAMPLE1.fastq | \

   bin/samtools view -uhS - | samtools sort -m 2000000000 - bams/SAMPLE1

   bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/SAMPLE1

You can check the use of parameters in the bwa manual. The result BAM file uses a compact binary format to represent the  

You can check the use of parameters in the bwa manual. The result BAM file uses a compact binary format to represent the