multithread support for gatk

Question

[bioguy24]

The below command is meant to use bqsr with multithreading:

gatk BaseRecalibrator --num_cpu_threads_per_data_thread=8 \
-I /home/cmccabe/Desktop/fastq/NA12878_marked_duplicates.bam \
-R /home/cmccabe/Desktop/fastq/resources/ucsc.hg19.fasta \
--known-sites /home/cmccabe/Desktop/fastq/fastq/resources/dbsnp_138.b37.vcf \
--known-sites /home/cmccabe/Desktop/fastq/resources/Mills_and_1000G_gold_standard.indels.hg19.vcf \
-O /home/cmccabe/Desktop/fastq/NA12878_recal_data.table

I have also tried nct 8 and both return an unrecognized exit code, so It does not appear to be supported or more likely I am not using it correctly? Thank you :).

[GenoMax]

What version of GATK?.

[bioguy24]

no sorry forgot to mention, the version is 4.0.6.0.... thank you :).

Answer 1

[GenoMax]

Update: Looks like you can't use nct with GATK 4.0. You have to use SPARK for parallelization.

[bioguy24]

Thank you very much :).