GATK recalibration confused, one step or two step?

[frankyue50]

Just based my reading
Previously, it was:
Quote:
java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa --DBSNP dbsnp132.txt -I input.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile input.recal_data.csv

java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -I input.marked.realigned.fixed.bam -T TableRecalibration --out input.marked.realigned.fixed.recal.bam -recalFile input.recal_data.csv

Then some suggested (http://seqanswers.com/forums/showthr...14038&page=5):
Quote:
java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -knowSites dbsnp132.txt -I input.marked.realigned.fixed.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate --out input.recal_data.csv

From GATK doc:
java -Xmx4g -jar GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-I my_reads.bam \
-R resources/Homo_sapiens_assembly18.fasta \
-knownSites bundle/hg18/dbsnp_132.hg18.vcf \
-knownSites another/optional/setOfSitesToMask.vcf \
-o recal_data.grp
with this additional step only if using several bam files (if I understand well the documentation: "PrintReads can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order" )
Quote:
java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T PrintReads \
-o output.bam \
-I input1.bam \
-I input2.bam \
--read_filter MappingQualityZero

What should I do?

[frankyue50]

Anyway, here is what I did:

java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R hg19.fa -knownSites 00-All.vcf -I input.nodup.realigned.fixed.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate --out input.csv

Will run the print read now

[vdauwera]

Hi there,

These tools have evolved slightly over the past few months, so make sure to read the latest documentation here: http://www.broadinstitute.org/gatk/guide/best-practices

Also, look at the presentations from the latest GATK workshop here:
http://www.broadinstitute.org/gatk/guide/events