How to extract alignment of one reads mapped to specific region?

[hujiacun]

Hi,
who can give me some suggestion?
The original data is pairend reads. I first get SAM file using BWA MM , and then BAM file using samtool. How can I get alignments of which first read is mapped to a specific region, such as chromosome 1( 100k-200k).

[dpryan]

Assuming you have a sorted and indexed BAM file:

samtools view -f 64 foo.bam chr1:100000-200000

[hujiacun]

Thanks!
If I want to extract alignments of anyone of the two pairend reads mapped to a specific region, how can I do it? Just as to get first read( flag 64), or second read(flag 128) mapped. I think "-f 192 "mean "first and second read" , how to assign to " first or second reads"?

[dpryan]

For first or second, just omit the -f option:

samtools view foo.bam chr1:100000-200000