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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