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How to use breakBandsAtMultiplesOf

I am using gatk3.7. combinegvcfs allows a large cohort to be called with genotypegvcfs. I also wish to use -L flag to combinegvcfs to shard the calculations by genomic location. Other guides also recommend '-ip 500' to ensure genotypegvcfs has context around the ends of the region to make correct calls.

Naively applying the above logic results in this warning:

WARN 13:19:15,638 CombineGVCFs - You have asked for an interval that cuts in the middle of one or more gVCF blocks. Please note that this will cause you to lose records that don't end within your interval.

--breakBandsAtMultiplesOf apparently solves this issue;

https://software.broadinstitute.org/gatk/documentation/tooldocs/3.7-0/org_broadinstitute_gatk_tools_walkers_variantutils_CombineGVCFs.php#--breakBandsAtMultiplesOf

However I am still getting the warning. I am unsure if my region logic is off by one, or the ip flag is having an effect, or something different?

Example region throwing a warning:

-L 9:50199356-62749194 --breakBandsAtMultiplesOf 12549839

50199356 % 12549839 == 0

Example python region generating code to try to deal with the off by one weirdness:

list(map(lambda s: (s[0],s[1]-1), pairwise(chain([1], range(0, chr_len, region_len)[1:], [chr_len + 1]))))

What is the correct way to shard gvcfs for genotypegvcfs? How do I use breakBandsAtMultiplesOf?

Thanks

Answers

  • Evan_BennEvan_Benn Member

    Here is a more full example of what I am doing:

    java -Xmx80g -Xms80g -jar GenomeAnalysisTK.jar -T CombineGVCFs \
        -R hs37d5x.fa \
        -o "$TMPDIR/{#}.combined.g.vcf.gz" \
        -ip 500 \
        -L 9:50199356-62749194 \
        --breakBandsAtMultiplesOf 12549839 \
        -V ...
    
    java -Xmx80g -Xms80g -jar GenomeAnalysisTK.jar \
     -T GenotypeGVCFs -nt 1 \
     -R hs37d5x.fa \
     -o $TMPDIR/output.vcf.gz \
     --dbsnp dbsnp_138.b37.vcf.gz \
     -L 9:50199356-62749194 \
     -V ...
    
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Evan_Benn

    We do not support GATK3 anymore. Please upgrade to our latest GATK4 v4.1.2.0

  • Evan_BennEvan_Benn Member

    Hello Bhanu,
    CombineGVCFs and breakBandsAtMultiplesOf are both in GATK4, but still undocumented. How do I use breakBandsAtMultiplesOf in GATK4?

    Thanks

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