Check if BAM is derived from pair-end or single-end reads?

I’m automating a pipeline and currently a user inputs as a parameter if the input BAM is from pair-end or single-end reads. I want to automatically check this. How can do I this?

Use the sam flag and samtools view -c -f 1 in.bam to test if your bam contains paired reads. ( 1= “read paired” See here )

You may also use samtools view -H. It will print you the header of the bam, including the command that was used for the alignment. Usually, paired-end data are separated into two fastq files, one for forward/reverse reads. Hence, if the alignment command shows two fastq files to be used, it was a paired-end alignment.

An example where BWA mem was used:

samtools view -H my.bam

@PG ID:bwa  PN:bwa  VN:0.7.12-r1044 CL:/opt/bwa-0.7.12/bwa mem -M -t 24 /Genomes/hg19/hg19.fasta in_1.fastq in_2.fastq
-----------------------------------------------------------------------------------------------------^---------^

where the general BWA mem paired-end command is (similar in Bowtie etc.):

./bwa mem -M -t *threads* indexedRefGenome.fasta in_1.fastq in_2.fastq > out.sam
-----------------------------------------------------^---------^