bamtools stats output

0

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5.5 years ago

GK1610 ▴ 110

I have merged 200 bam files using bamtools. When I use bamtools stats options on the merged bam file, I get 117% each for forward strands and reverser strands. why would that happen? it should be 50% for both strands.

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Stats for BAM file(s):
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Total reads:       3158957612
Mapped reads:      3158957612   (100%)
Forward strand:    3726962454   (117.981%)
Reverse strand:    3726962454   (117.981%)
Failed QC:         0    (0%)
Duplicates:        0    (0%)
Paired-end reads:  3158957612   (100%)
'Proper-pairs':    3158957612   (100%)
Both pairs mapped: 3158957612   (100%)
Read 1:            3726962454
Read 2:            3726962454
Singletons:        0    (0%)

alignment sequencing • 3.4k views

ADD COMMENT • link 5.5 years ago by GK1610 ▴ 110

2

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Looked weird. bamtools looked a bit old. Could you please check the stats with samtools flagstat ?

fin swimmer

ADD REPLY • link 5.5 years ago by finswimmer 16k

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