Daniel:Notebook/GenomeMiner/2013-7-22: Difference between revisions
Jump to navigation
Jump to search
>Djacobse No edit summary |
>Djacobse No edit summary |
||
Line 3: | Line 3: | ||
[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
'''1. Converting | '''1. Converting SAM to BAM''' | ||
samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam | samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam | ||
Line 14: | Line 14: | ||
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155 | 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 |
Revision as of 20:52, 22 July 2013
HL155
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