== Mining, summarizing, and processing SAM/BAM files ==

Many of these involve [http://samtools.sourceforge.net/samtools.shtml | samtools]

=== Convert, sort, and/or index ===


{{{
Convert SAM to BAM:
 samtools view -bS -o foo.bam foo.sam
}}}

{{{
Convert BAM to SAM:
 samtools view -h -o foo.sam foo.bam
}}}
{{{
Sort BAM file (where ".bam" is added to "foo.sorted")
 samtools sort foo.bam foo.sorted
}}}
{{{
Index a sorted BAM file (which creates foo.sorted.bam.bai):
 samtools index foo.sorted.bam
    
Both foo.sorted.bam and foo.sorted.bam.bai are needed for visualization.
 }}}  

=== Count the number of mapped reads ===

{{{
samtools flagstat mapped_unmapped.bam
}}}

=== Count the number of mapped reads by chromosome ===

{{{
Method 1 (all chromosomes)
1 - Index the BAM file: 
 samtools index mapped_reads.bam
2 - Get index statistics (including the number of mapped reads in the third column: 
 samtools idxstats mapped_reads.bam
}}}

{{{
Method 2 (one chromosome, without a BAM index)
From SAM
 awk -F"\t" '$3 == "chr2" {print $1}' mapped_reads.sam | sort -u | wc -l
From BAM
 samtools view mapped_reads.bam | awk -F"\t" '$3 == "chr2" {print $1}' | sort -u | wc -l
}}}

=== Remove unmapped reads ===


{{{
samtools view -hS -F 4 mapped_unmapped.sam > mapped_only.sam
}}}


=== How many multiple/uniquely mapped reads are in a bam/sam file?

{{{
bam_stat.py -i mapped_reads.bam >& bam_stat.out.txt
}}}