Question: samtool flagstat question
0
gravatar for alex
4.6 years ago by
alex200
United States
alex200 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!

samtools bam • 1.8k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 4.6 years ago by alex200
2
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

Realignment and such won't change these metrics. Realignment just locally realigns things and typically the assigned MAPQ values don't change (unmapped mates etc. also won't change). Recalibration typically affects only base qualities. I should note that recalibration is typically not needed anymore (the same goes for realignment if you're using something like GATK's haplotype caller).

ADD COMMENTlink written 4.6 years ago by Devon Ryan93k
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