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  • 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, 12:31 AM.

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