Hello everyone, I had been using GATK3.7 until last Septemeber to identify variants from human whole exome sequencing samples. However, recently, our institute has upgraded to GATK4.1. In accordance with GATK3.7, our pipeline identified variants from the
bam file, which was then recalibrated and the BQSR table was used with
GATK PrintReads (with -BQSR option) along with the source bam file to createa recalibrated bam file which was then used to identify variants after recalibration.
I noticed that in
GATK4.1 the -BQSR option has been redacted for the PrintReads functionality. It would be extremely helpful if someone could give me a solution to this issue.
Thanks in advance.
P.S. Since this concern is of urgency, this has been reposted from the GATK forum https://gatk.broadinstitute.org/hc/en-us/community/posts/360076435471-How-do-I-recalibrate-variants-in-GATK4-1-as-compared-to-GATK3-7