Obtain Number of PE Reads in BAM file Mapped to Each Chromosome

Question

[ssm87]

Given a sorted/indexed BAM file (or SAM file if that is easier) which was produced by aligning PE reads to a reference genome, how can I enumerate the:

1) number of read pairs with both reads mapping to a particular chromosome

2) number of read pairs with only one of the reads mapping to a particular chromosome

i.e. scenario #1

--R1--> <--R2--

scenario #2

--R1-->

OR

<--R2--

Answer 1

[goodez]

1) Number of properly paired, mapped reads only on chr1:

samtools view -f 1 -F 12 -b file.bam chr1 | wc -l

2) It's possible for only first pair to be unmapped, or only second pair, so combine two commands:

samtools view -f 4 -F 264 file.bam chr1 | wc -l   

samtools view -f 8 -F 260 file.bam chr1 | wc -l

Add those two output together to get total number of reads where one pair is unmapped

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Change the chromosome name as needed, this example was for chr1