diffrence between number of reads in fastqc reports and collectalignmentsummarymetrics of Picard

Question

[kk.mahsa]

hi everyone

i have 4 fastq files (two lane correspond to one organism), after filtration of reads, FastQC tell me that total number of reads is 628748302, i mapped them to reference genome and merged resulted two bam file and then sorted it. Now when i run collectalignmentsummarymetrics of Picard to get total and mapped read number, Picard tell me that total number of reads is 628601638. also when i used samtools flagstat, number of total reads counted 629770210, which number is correct?

thanks

[GenoMax]

See past threads on this question:
How come the QC-passed reads from samtools flagstat is different from FASTQ (R1+R2) read count?
Samtools flagstat number of reads do not match actual total number of reads.