1.several tool sets have been created to manipulate SAM/BAM files:

samtools , bamtools , picard  

2.how can I select from or filter data from BAM files?

2.1  clarify some wording:

 selecting means to keep alignments that match a condition

filter means to remove alignments that match a condition

-f   (flag) includes only alignments where the bits match the bits in the flag

-F  (flag) includes only alignments where the bits do not match the bits in the flag

2.2 recall what flag 4 means and how to use it :

samtools flags 4   #表示unmap reads

samtools view -f 4 file.bam | head   # select and view the unmapped reads

samtools view -f 4 file.bam | wc -l #count the unmapped reads

samtools view -c -f 4 file.bam  # count the unmapped reads

samtools view -c  -F 4 file.bam # count the mapped reads

samtools view -b -F 4 file.bam > file_mapped_reads # separate unmapped reads

samtools view -c -f 16 file.bam # reads that align to reverse strand

samtools view -c -F 4 -f 16 file.bam # reads that align to reverse stand and not unmapped.

samtools view -c -F 20 file.bam # reads that align to forwards strand and are not unmapped

samtools view -b -f 4 file.bam > file_mapped_reads # separate mapped reads

2.3 Get an overview of the alignments in a BAM file

samtools flagstat file.bam # produces a report on flags

samtools idxstats file.bam # produces a report on how many reads align to each chromosome

bamtools stats -in file.bam # produces a report on flags

2.4 how do I filter on mapping quality?

The mapping quality column contains a number that the aligner fillls in . This number is rarely an objection quantity , it rather reflects a subjective value designated by the tool developer.

smatools view -c -q 1 file.bam  #select uniquely mapped reads when these were a aligned with BWA

smatools view -c -q 1 -F 4 -F 16 file.bam # mapping quality over 1 and on the forward strand (file.bam by BWA)

2.5 how can I find out the depth of coverage ?

samtools depth file.bam  | head  # compute the depth of coverage, compute the number of reads that overlap each base .

samtools depth -a file.bam | head  # ask for all position and you can verify that it starts at 1

smatools depth file.bam | sort -k 3 -rn | head  # sort by depth