Hi I would like to separate 1/2 mates of a paired-end bam file.
To see first mate:
samtools view -F 0x40 in.bam
To see second mate:
samtools view -F 0x80 in.bam
but it returns the following as first mate (0x40):
H0544AFXX:1:11101:8739:1038 163 chr3 17908775 3 1S74M = 17909029 330 ...
and for example this one as second (
83chr3 17909029 3 75M = 17908775 -330
while Flag 163 means:
read paired read mapped in proper pair mate reverse strand second in pair
read paired read mapped in proper pair read reverse strand
It would be great if somebody could clarify this issue. thanks