Daniel:Notebook/GenomeMiner/2013-7-22: Difference between revisions
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
==SAMtools== | |||
'''1. Converting SAM to BAM''' | '''1. Converting SAM to BAM''' |
Revision as of 20:53, 22 July 2013
HL155
SAMtools
1. Converting SAM to BAM
samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam
2. Sorting BAM file
samtools sort hrcp_hl155.bam hrcp_sorted_hl155
Alternate Pipeline (Can be used instead of 1 and 2)
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155
3. Create BAM index file
samtools index hrcp_sorted_hl155.bam hrcp_sorted_hl155.bai