Changes

   foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)

   foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)

   echo $file

   echo $file

   bin/bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai

   bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai

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

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

     bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file

     samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file

   bin/samtools index bams/$file.bam

   samtools index bams/$file.bam

   end

   end

  for file in `ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`;

  for file in `ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`;

   do echo $file;

   do echo $file;

   bin/bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai;

   bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai;

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

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

     bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file;

     samtools view -uhS - | samtools sort -m 2000000000 - bams/$file;

   bin/samtools index bams/$file.bam;

   samtools index bams/$file.bam;

  done

  done