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failed while using GATK3.8.1 Baserecalibrator with -nct

Hi, GATK team,
I am using GATK 3.8.1 BASERECALIBRATOR in handling the targeted region sequencing data.
And i want to speedup the process so I add the -nct command and failed with an empty file eventually.
please find the command and the result I ran as following, and please give me some suggestions.
thanks a lot.

java -jar -Xmx64G /usr/GenomeAnalysisTK.jar -T BaseRecalibrator\
-nct 10 \
-R ${reference}\
-I ${inputbam}/${SM}.sorted.bam\
-knownSites ${gatk_bundle}/dbsnp_138.hg19.vcf\
-knownSites ${gatk_bundle}/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf\
-o ${outputdir}/BQSR/${SM}_first_recal.table\
-L ${bedfile}

java -jar -Xmx64G /usr/GenomeAnalysisTK.jar -T BaseRecalibrator \
-R ${reference} \
-I ${inputbam}/${SM}.sorted.bam \
-knownSites $gatk_bundle/dbsnp_138.hg19.vcf \
-knownSites $gatk_bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
-BQSR ${outputdir}/BQSR/${SM}_first_recal.table \
-o ${outputdir}/BQSR/${SM}_second_recal.table
.....

Result:

Answers

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