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Created 2016-03-15 06:05:14 | Updated | Tags: unifiedgenotyper pooling

Comments (4)

I've got a pool of 80 individuals sequencing data. Each individual doesn't have index, so that i have just one fastq file and bam file that i cannot sort any sample data from it.

I try to use GATK UnifiedGenotyper v3.3 including "-ploid" option There're some questions.

  1. command : java -Xmx100g -jar /ruby/Tools/GATK/GenomeAnalysisTK-3.3/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ./Ref.fasta -I 1.bam -o 1_unified.vcf --sample_ploidy 160 -minIndelFrac 0.05 --genotype_likelihoods_model BOTH -pnrm EXACT_GENERAL_PLOIDY -nct 4 -nt 10

--sample_ploidy = 160 = 80 (pooling 80 individuals) * ploid ( diploid, 2 ) bamfile size = 3.4GB

SERVER SPEC : CPU core = 40x memory = 256G

I've started the process 4 days ago. The progress percent is 0.3%, and remain time is 176.9 weeks. I think it's too slow to complete. I just wonder how long takes time to process GATK UnifiedGenotyper on that data. Is there any recommendations to improve this job?

Created 2015-08-31 11:58:59 | Updated | Tags: baserecalibrator best-practices ploidy pooling

Comments (3)

Dear GATK Team,

baserecalibrator is in the newest Best Practices recommendations. Does this tool support or would you recommend it's usage for samples with ploidy higher then 2 (e.g. pooled samples)?

Thanks! Bernt

Created 2013-01-09 11:16:39 | Updated 2013-01-09 11:17:10 | Tags: exome pooling lanes

Comments (2)


I have exome data run on two lanes per library is it better to combine the lanes into one or to run each lane independently through GATK? What are the pros and cons? Many thanks