Mining, summarizing, and processing SAM/BAM files

Many of these involve ​| 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