BaseRecalibrator
Posted in Ask the team | Last updated on


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Hi: i met errors in my recalibration process. every time errors occur, the messages put "don't post the errors",and then i can find solution in FAQ or furom. however, this time, it tells me to post the errors. i tried to find sulotion, but failed. i am new to GATK, and know little about java.

here is the command:

nohup java -Xmx50g -Djava.io.tmpdir=/tmp\ -jar $GATKdir/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -R ~/data/ReferAll/sortedIndex/ucsc.hg19.sorted.fasta \ -I ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam \ -knownSites ~/data/ReferAll/bundle/dbsnp_137.hg19.sorted.vcf \ -knownSites ~/data/ReferAll/bundle/1000G_phase1.indels.hg19.sorted.vcf \ -knownSites ~/data/ReferAll/bundle/Mills_and_1000G_gold_standard.indels.hg19.sorted.vcf \ -o ~/projects/TWINS/WGC007813/WGC007813.sai.sam.dedup.realigned.bam.recal.grp \

~/projects/TWINS/WGC007813/no.BaseRecalibrator.out &

and this is the errors message!


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