Question: samtool flagstat question
0
alex • 200 wrote:
Hi,
So I have created a bam from a NIST sample. I did realignment and recalibration but the flagstat numbers don't change. Should I be worried? Thanks!
samtools flagstat NA12878-test1_S1_L001_R1_001.bam 55456561 + 0 in total (QC-passed reads + QC-failed reads) 5895280 + 0 duplicates 55320108 + 0 mapped (99.75%:-nan%) 55456561 + 0 paired in sequencing 27727985 + 0 read1 27728576 + 0 read2 55020320 + 0 properly paired (99.21%:-nan%) 55233536 + 0 with itself and mate mapped 86572 + 0 singletons (0.16%:-nan%) 67065 + 0 with mate mapped to a different chr 33459 + 0 with mate mapped to a different chr (mapQ>=5) samtools flagstat NA12878-test1_S1_L001_R1_001.realigned.bam 55456561 + 0 in total (QC-passed reads + QC-failed reads) 5895280 + 0 duplicates 55320108 + 0 mapped (99.75%:-nan%) 55456561 + 0 paired in sequencing 27727985 + 0 read1 27728576 + 0 read2 55020320 + 0 properly paired (99.21%:-nan%) 55233536 + 0 with itself and mate mapped 86572 + 0 singletons (0.16%:-nan%) 67065 + 0 with mate mapped to a different chr 33459 + 0 with mate mapped to a different chr (mapQ>=5) samtools flagstat NA12878-test1_S1_L001_R1_001.realigned.recalibrated.bam 55456561 + 0 in total (QC-passed reads + QC-failed reads) 5895280 + 0 duplicates 55320108 + 0 mapped (99.75%:-nan%) 55456561 + 0 paired in sequencing 27727985 + 0 read1 27728576 + 0 read2 55020320 + 0 properly paired (99.21%:-nan%) 55233536 + 0 with itself and mate mapped 86572 + 0 singletons (0.16%:-nan%) 67065 + 0 with mate mapped to a different chr 33459 + 0 with mate mapped to a different chr (mapQ>=5)
Thanks!
