Hello,
I am trying to use the samtools flagstat in order to generate the statistics.
The bam files are generated from bioscope and here's what i get
samtools flagstat myFile.bam > myFile.stats
3706062915 + 0 in total (QC-passed reads + QC-failed reads)
1284337071 + 0 duplicates
3706062915 + 0 mapped (100.00%:nan%)
2988908908 + 0 paired in sequencing
1480626898 + 0 read1
1508282010 + 0 read2
1978289514 + 0 properly paired (66.19%:nan%)
2539279046 + 0 with itself and mate mapped
449629862 + 0 singletons (15.04%:nan%)
476297856 + 0 with mate mapped to a different chr
209157066 + 0 with mate mapped to a different chr (mapQ>=5)
Is this output in the right format ?? Is something wrong with my input file ?
Thank you,
Regards,
Nandini
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