Now need to use Pindel(split-read approach to identify CNV). I'm just wondering how I can extract one-end mapped reads from BWA result? Does samtools have such options, or we need to extract by parsing the sam/bam file according to flags?

Thanks

Edit: Just another question. After BWA running, I actually do the filtering to pick out those mapping with MAPQ > 20; will this affect picking up unmapped/one-end mapped reads?

I guess this won't affect finding one-end mapped reads; but those two-end unmapped reads cannot be picked up.

Edit again: This is my another question: I ran the command:

samtools view -u -f 8 -F 260 map.bam  > oneEndMapped.bam

And let's look at the line of oneEndMapped.bam:

HWI-ST150_0129:2:1:1414:2357#0    153    chr1    154432976    37    101M    =    154432976    0    ACATACATATGTATGTAATATGTGATTATTACTGGTGGTTTGCTAAATAATGACAAATGGAAAAAAATATATGTCATCCAAAGAGAGCCACTGTTAATTTT    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBdc^ddcacc\TdcdddddYbe_dffddcffcffecedecedaeeeedd\def^ffeff`c    RG:Z:101127_s_2    XT:A:U    NM:i:2    SM:i:37    AM:i:0    X0:i:1    X1:i:0    XM:i:2    XO:i:0    XG:i:0    MD:Z:16G20A63

How to interpret this: To me, this looks like both ends have the same sequences, and map to the same position. (leftmost coordinate of one read; and leftmost of another). Why do we say this represents one read maps while the other one doesn't map? To describe "one read maps while the other one doesn't map", in my mind, it should be like:

HWI-ST150_0129:2:1:1414:2357#0    153    chr1    154432976    37    101M    =    *   *

Also running

samtools view -u  -f 4 -F 264 map.bam  > oneEndUnmapped.bam

This oneEndUnmapped.bam is only 8K, means nothing. I don't quite understand this.

thx