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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 \
and this is the errors message!