Hi,
I run
samtools view -bh old.bam > new.bam
the new.bam is 98G while the old.bam is 110G.
But the flatstat for old.bam is
713835589 + 0 in total (QC-passed reads + QC-failed reads)
5098877 + 0 secondary
0 + 0 supplementary
45662312 + 0 duplicates
706481423 + 0 mapped (98.97% : N/A)
708736712 + 0 paired in sequencing
354368356 + 0 read1
354368356 + 0 read2
682853462 + 0 properly paired (96.35% : N/A)
696021484 + 0 with itself and mate mapped
5361062 + 0 singletons (0.76% : N/A)
9163046 + 0 with mate mapped to a different chr
4873946 + 0 with mate mapped to a different chr (mapQ>=5)
The flagstat fo new.bam is
736285019 + 0 in total (QC-passed reads + QC-failed reads)
5388533 + 0 secondary
0 + 0 supplementary
30551497 + 0 duplicates
730966740 + 0 mapped (99.28% : N/A)
730896486 + 0 paired in sequencing
365448243 + 0 read1
365448243 + 0 read2
709064844 + 0 properly paired (97.01% : N/A)
722413152 + 0 with itself and mate mapped
3165055 + 0 singletons (0.43% : N/A)
9176396 + 0 with mate mapped to a different chr
4811953 + 0 with mate mapped to a different chr (mapQ>=5)
There are more reads in new.bam with smaller file size. A little confused
what happen here.
Best,
Gang
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Samtools-help mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/samtools-help
