Thank you for the answer.
I have tried running CountReads and i got the same number of reads as samtools or wc -l file.sam.
This means that the log message by Mutect2 was not correct.
java -jar GenomeAnalysisTK.jar -R referenc…
Thnks for the reply. I think there is something strange in counting the number of reads.
I counted the reads using wc -l file.sam and samtools flagstat
I got same number of reads using both wc -l file.sam and samtools flagstat