Recalibrating variants in GATK4.1 as compared to GATK3.7

Question

[vinayjrao]

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

Answer 1

[DareDevil]

#Recalibrating bases based on known Indels, snp data
gatk BaseRecalibrator --input sample1_sorted_MarkDups.bam \
    --known-sites $MillsIndels \
    --known-sites $Indels1kGenome \
    --known-sites $DBSNP \
    --output sample1_recal_data.table \
    --reference $reference 


# Applying the recalibrated base info on Bam
gatk ApplyBQSR --input sample1_sorted_MarkDups.bam \
    --reference $reference \
    --bqsr-recal-file sample1_recal_data.table \
    --output sample1_sorted.deduped.bqsr.bam

[vinayjrao]

Thank you very much for your reply however, does this imply that ApplyBQSR is an alternate to PrintReads with respect to my request, or do I have to still use PrintReads?

[DareDevil]

PrintReads is no longer available in gatk4 and ApplyBQSR does the same functionality of PrintReads

[vinayjrao]

Thank you once again.