Question: samtools flagstat interpretation
1
gravatar for dnyanada.gokhale
2.6 years ago by
dnyanada.gokhale10 wrote:

Hi All, I am trying to run samtools flagstat to determine whether my bam files contain duplicates. I do not have the fastqc files for these bams. They were already aligned, using BWA I believe and sent over. The samtools flagstat statistics before and after running the mark duplicates tool in Picard are as follows.

Samtools flagstat before running Mark duplicates
54020790 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
51506397 + 0 mapped (95.35%:-nan%)
54020790 + 0 paired in sequencing
27010395 + 0 read1
27010395 + 0 read2
50485840 + 0 properly paired (93.46%:-nan%)
50592454 + 0 with itself and mate mapped
913943 + 0 singletons (1.69%:-nan%)
63320 + 0 with mate mapped to a different chr
48093 + 0 with mate mapped to a different chr (mapQ>=5)

Samtools flagstat after running Mark duplicates in as follows
54020790 + 0 in total (QC-passed reads + QC-failed reads)
2723962 + 0 duplicates
51506397 + 0 mapped (95.35%:-nan%)
54020790 + 0 paired in sequencing
27010395 + 0 read1
27010395 + 0 read2
50485840 + 0 properly paired (93.46%:-nan%)
50592454 + 0 with itself and mate mapped
913943 + 0 singletons (1.69%:-nan%)
63320 + 0 with mate mapped to a different chr
48093 + 0 with mate mapped to a different chr (mapQ>=5)

So based on these results I am assuming that in the earlier bam file the duplicates had not been marked. Am I right in assuming this. Also if someone could provide a simple explanation of how to interpret the samtools flagstat tools it would be really helpful. Thanks

ADD COMMENTlink modified 2.6 years ago by Devon Ryan86k • written 2.6 years ago by dnyanada.gokhale10
0
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

You're correct that duplicates weren't marked in the original file.

Regarding the flagstat output, just mention what portion of it is unclear and someone can reply specifically to that.

ADD COMMENTlink written 2.6 years ago by Devon Ryan86k

Thank you so much, That was my major confusion since I only received bam files not the fastqc ones.

ADD REPLYlink written 2.6 years ago by dnyanada.gokhale10
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