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====== Processing Sam output for IGV ======
To see sam file in igv
NOTE !! The index file MUST be in the same directory as the file.

1) load samtools module
<code>
module load samtools
</code>

2) Create an index for the genome fasta file
<code>
samtools faidx Mesculenta_147.fa
</code>

3) For each sam files, convert to bam file
<code>
samtools view -S -b NDL06-132.sam > NDL06-132.bam
</code>

4) sort each bam file
<code>
samtools sort NDL06-132.bam NDL06-132.bam.sorted
</code>

5) create index for each bam file
<code>
samtools index NDL06-132.bam.sorted.bam
</code>