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Old 08-17-2021, 12:09 AM   #1
greekkey
Junior Member
 
Location: Tokyo

Join Date: Sep 2012
Posts: 7
Default AnalyzeCovariates in GATK4.2

Hi, does anyone use AnalyzeCovariates under GATK4.2.0.0? It seems that we should be able to perform BaseRecalibrator twice to get the -before and -after "recal_data.table" files and compare using AnalyzeCovariates. However, when I tried the following commands,

----------------------------------------------------------------------------------------------------------------
# First BQSR (Already done)
# java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
# BaseRecalibrator \
# -R ${CKXLhg38} \
# -I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
# --known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
# --known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
# -O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table

# Second BQSR
java -jar ${RJLJ}/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar \
BaseRecalibrator \
-R ${CKXLhg38} \
-I ${ZLJ}/6_DedupedBam/${Takara_ID}_${Sample_Name}_aligned_fixmated_sorted_deduped.bam \
--known-sites ${GATKFiles}/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
--known-sites ${GATKFiles}/bundle/hg38/dbsnp_146.hg38.vcf.gz \
-bqsr ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.table*\
-O ${ZLJ}/9_BQSRrecalDATAtable/${Takara_ID}_${Sample_Name}_merged_realigned_recal_data.after.table
---------------------------------------------------------------------------------------------------------------------------------------------------------------

I got an error saying that

***********************************************************************

A USER ERROR has occurred: -bqsr is not a recognized option

***********************************************************************

So how can I get the -after "recal_data.table" file? Or is there any other method to perform quality check for bam files before going to variant calling?
Thanks in advance!

Last edited by greekkey; 08-17-2021 at 12:31 AM.
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