Daniel:Notebook/GenomeMiner/2013-7-22

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HL155[edit]

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SAMtools[edit]

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

4. View Mapped Reads Only

samtools view -h -F 4 hrcp_sorted_hl155.bam > hrcp_mapped_hl155.bam