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Any tips for speed up the HaplotypeCaller?

skblazerskblazer Member
edited August 2012 in Ask the GATK team

Hi,

I'm trying HaplotypeCaller of GATK2.1.2, but it looks very slow for my case.
For example, it requires several weeks to walk through the 200M reference for a population of three resequencing samples (10-20x each), any suggestions to help deal with this? Is this a normal speed or my server has problem to load this.

java -Xmx32g -jar ~/tools/GenomeAnalysisTK-2.1-2-g916702e/GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -dcov 100 --heterozygosity 0.01 -U -S SILENT -rf BadCigar -stand_emit_conf 10 -baq CALCULATE_AS_NECESSARY -o popBZ_Haplotype.vcf -I BAMs/BZ25.bam -I BAMs/BZ26.bam -I BAMs/BZ27.bam

INFO 12:16:47,106 TraversalEngine - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining

INFO 12:21:51,400 TraversalEngine - scaffold1:33007 3.30e+04 5.1 m 2.6 h 0.0% 3.8 w 3.8 w

INFO 12:28:32,030 TraversalEngine - scaffold1:50007 5.00e+04 11.8 m 3.9 h 0.0% 5.8 w 5.8 w

INFO 12:34:27,076 TraversalEngine - scaffold1:66007 6.60e+04 17.7 m 4.5 h 0.0% 6.6 w 6.6 w

INFO 12:39:58,655 TraversalEngine - scaffold1:82007 8.20e+04 23.2 m 4.7 h 0.0% 7.0 w 7.0 w

INFO 12:45:34,501 TraversalEngine - scaffold1:99007 9.90e+04 28.8 m 4.8 h 0.0% 7.2 w 7.2 w

Best,
SK

Best Answer

  • Mark_DePristoMark_DePristo Broad Institute admin
    Accepted Answer

    A few recommendation. Using -U suggests your BAM may be malformed, and potentially breaking the GATK in strange ways. If you don't have a valid BAM there's no guarantee what will happen.

    There's no reason for BAQ at all. I've just added a FORBIDDEN tag for the BAQ to HC.

Answers

  • Mark_DePristoMark_DePristo Broad InstituteMember admin
    Accepted Answer

    A few recommendation. Using -U suggests your BAM may be malformed, and potentially breaking the GATK in strange ways. If you don't have a valid BAM there's no guarantee what will happen.

    There's no reason for BAQ at all. I've just added a FORBIDDEN tag for the BAQ to HC.

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