Changes between Version 26 and Version 27 of SOPs/variant_calling_GATK


Ignore:
Timestamp:
10/31/25 14:35:16 (3 days ago)
Author:
kdesilva
Comment:

--

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  • SOPs/variant_calling_GATK

    v26 v27  
    4343May Need "VALIDATION_STRINGENCY=LENIENT" if you get  \\
    4444Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: ... MAPQ should be 0 for unmapped read. \\
    45   * bsub java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=Reads_1.bwa.sorted.bam O=Reads_1.bwa.dedup.bam M=Reads_1.bwa.dedup.txt VALIDATION_STRINGENCY=LENIENT
     45  * sbatch --job-name=MarkDuplicates --wrap="java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=Reads_1.bwa.sorted.bam O=Reads_1.bwa.dedup.bam M=Reads_1.bwa.dedup.txt VALIDATION_STRINGENCY=LENIENT"
    4646\\
    47477 - '''Add Read Group header information to each BAM file''' (or GATK won't let you continue) \\
    4848Run Picard Tools' [[https://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups|AddOrReplaceReadGroups]] on each sample. \\
    4949Specify RGSM (Read Group sample), RGLB (Read Group Library), RGPL (Read Group platform), and RGPU (Read Group platform unit [e.g. run barcode])
    50   * bsub java -jar /usr/local/share/picard-tools/picard.jar AddOrReplaceReadGroups I=Reads_1.bwa.dedup.bam O=Reads_1.bwa.dedup.good.bam RGSM=My_sample RGLB=My_project RGPL=illumina RGPU=none VALIDATION_STRINGENCY=LENIENT
     50  * sbatch --job-name=AddRG --wrap="java -jar /usr/local/share/picard-tools/picard.jar AddOrReplaceReadGroups I=Reads_1.bwa.dedup.bam O=Reads_1.bwa.dedup.good.bam RGSM=My_sample RGLB=My_project RGPL=illumina RGPU=none VALIDATION_STRINGENCY=LENIENT"
    5151\\
    52528 - '''Index BAM file(s)''' with [[http://samtools.sourceforge.net/samtools.shtml|samtools]] (optional; for IGV viewing)
    53   * bsub samtools index Reads_1.bwa.dedup.good.bam
     53  * sbatch --job-name=samtools_index --wrap="samtools index Reads_1.bwa.dedup.good.bam"
    5454\\
    55559 - '''Run Indel Realignment''' (with [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_RealignerTargetCreator.php|RealignerTargetCreator]] and [[https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php|IndelRealigner]]) \\
    … …  
    6868  * Example 4: java -jar GenomeAnalysisTK.jar -T AnalyzeCovariates -R human.fasta -before recal.table -after after_recal.table -plots recal_plots.pdf
    6969All applied to our sample data:
    70   * bsub java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -o Reads_1.bwa.recal_data.txt -knownSites SNPs_from_NCBI.sorted.vcf
    71   * bsub java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T PrintReads -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.dedup.realigned.recal.bam
    72   * bsub java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -knownSites SNPs_from_NCBI.sorted.vcf -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.after_recal.txt
    73   * bsub java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /path/to/genome/genome.fa -before Reads_1.bwa.recal_data.txt -after Reads_1.bwa.after_recal.txt -plots Reads_1.bwa.recal_plots.pdf
     70  * sbatch --job-name=GATK_BaseRecal --wrap="java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -o Reads_1.bwa.recal_data.txt -knownSites SNPs_from_NCBI.sorted.vcf"
     71  * sbatch --job-name=GATK_PrintReads --wrap="java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T PrintReads -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.dedup.realigned.recal.bam"
     72  * sbatch --job-name=GATK_BaseRecal2 --wrap="java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T BaseRecalibrator -I Reads_1.bwa.dedup.realigned.bam -R /path/to/genome/genome.fa -knownSites SNPs_from_NCBI.sorted.vcf -BQSR Reads_1.bwa.recal_data.txt -o Reads_1.bwa.after_recal.txt"
     73  * sbatch --job-name=GATK_AnalyzeCov --wrap="java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T AnalyzeCovariates -R /path/to/genome/genome.fa -before Reads_1.bwa.recal_data.txt -after Reads_1.bwa.after_recal.txt -plots Reads_1.bwa.recal_plots.pdf"
    7474
    7575\\