Hi.
I am running Haplotyper with the below command.
java -jar /usr/local/lib/GenomeAnalysisTK.jar -T HaplotypeCaller -R /media/data1/02_SNP_flanking_GC_content/am45new.fasta -nct 1 -I HDB148.sorted.stampy.rg.dp.gatk.BQSR.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 --sample_ploidy 24 -o HDB148_raw_variants.vcf
But i am getting the error of insufficient memory allocated. I am having 12 diploid pooled samples.
I am having the files with higher number of pooled samples
Any suggestion in this is highly appreciated.
Thank you.
Tanushree