ApplyBQSR without -L will add more reads

[nathanLauHKGI]

Please find attached samtools stats file.

sample1.markdup.sorted.stats is before BQSR and ApplyBQSR sample1.stats is after BQSR and ApplyBQSR

As you can see, before ApplyBQSR (NA12878-P.markdup.sorted.stats.txt), the raw total sequences is 119998832 After ApplyBQSR (NA12878-P.stats.txt), the raw total sequences is 120169477

gatk_applyBQSR_error.log is the log file of the applyBQSR step

Do you have any ideas?

gatk_applyBQSR_error.log NA12878-P.markdup.sorted.stats.txt NA12878-P.stats.txt