To see sam file in igv NOTE !! The index file MUST be in the same directory as the file.

1) load samtools module

module load samtools

2) Create an index for the genome fasta file

samtools faidx Mesculenta_147.fa

3) For each sam files, convert to bam file

samtools view -S -b NDL06-132.sam > NDL06-132.bam

4) sort each bam file

samtools sort NDL06-132.bam NDL06-132.bam.sorted

5) create index for each bam file

samtools index NDL06-132.bam.sorted.bam