samtools flagstat and ViewSam ALIGNMENT_STATUS=Aligned

[fabrice]

I am using and samtools flagstat to statistc how many reads mapped in my s_4.bam (produced by eland, convert from export files).

samtools flagstat s_4.bam

Then I used picard.

java -jar ViewSam.jar INPUT=s_4.bam ALIGNMENT_STATUS=Aligned PF_STATUS=All VALIDATION_STRINGENCY=SILENT > s_4_Aligned_reads.sam

I expected that the line number of s_4_Aligned_reads.sam will be equal to mapped number report by samtools. But it is biger than the number report by samtools.

Does any one know why?

samtools flagstat s_4.bam

43055574 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
8834640 + 0 mapped (20.52%:nan%)
43055574 + 0 paired in sequencing
21527787 + 0 read1
21527787 + 0 read2
0 + 0 properly paired (0.00%:nan%)
5208944 + 0 with itself and mate mapped
3625696 + 0 singletons (8.42%:nan%)
117012 + 0 with mate mapped to a different chr
112688 + 0 with mate mapped to a different chr (mapQ>=5)

wc -l s_4_Aligned_reads.sam
11789604 s_4_Aligned_reads.sam



Thanks.