This is a test version of Biostars. For the public version, visit https://www.biostars.org.
samtool flagstat question

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!

bam samtools
• 3,355 views • link
updated by Ram Ram • written by alex alex

1 answer

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).

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this