Entering edit mode
5.7 years ago
bioguy24
▴
230
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 :).
What version of GATK?.
no sorry forgot to mention, the version is 4.0.6.0.... thank you :).