以下命令解决了GATK4按照目前GATK3来做AnalyzeCovariates的报错：
“A USER ERROR has occurred: b is not a recognized option”
My commands are as below:
# BQSR - first pass
gatk BaseRecalibrator \
-I=sample_dedup.bam \
-R=/Reference/genome_ref.fasta \
--known-sites mysnp.vcf \
-O=**sample_recal_pass1.tabl**
gatk ApplyBQSR \
-I sample_dedup.bam \
-R /Reference/genome_ref.fasta \
--bqsr-recal-file **sample_recal_pass1.tabl** \
-O **sample_dedup.recal.pass1.bam**
# BQSR - second pass
gatk BaseRecalibrator \
-I **sample_dedup.recal.pass1.bam** \
-R /Reference/genome_ref.fasta \
--known-sites mysnp.vcf \
-O **sample_recal_pass2.tabl**
gatk ApplyBQSR \
-I sample_dedup.recal.pass1.bam \
-R /Reference/genome_ref.fasta \
--bqsr-recal-file **sample_recal_pass2.tabl** \
-O **sample_dedup.recal.pass2.bam**
##Then use the first pass BAM file `sample_dedup.recal.pass1.bam` for downstream processing.
# compare outputs
gatk AnalyzeCovariates \
--before-report-file **sample_recal_pass1.tabl** \
--after-report-file **sample_recal_pass2.tabl** \
--plots-report-file output.pdf
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GATK4--AnalyzeCovariates报错
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