Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK4 ( Mutect2 --germline-resource option Simoner Bioinformatics 4 08-03-2020 05:27 AM
bwa GATK4 read group issues wbsimey Bioinformatics 2 01-22-2020 08:38 AM
GATK4, bash script... step CreateSequenceGroupingTSV echo manolis Bioinformatics 1 01-24-2018 01:06 PM

Thread Tools
Old 08-17-2021, 12:09 AM   #1
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- \
# 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- \
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.
greekkey is offline   Reply With Quote

analyzecovariates, gatk4.2.0.0

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:41 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO