Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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!