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order of bam is different from order of vcf in GATK(UnifiedGenotyper v3.4-46-gbc02625)

hi, guys:
i have a problem about UnifiedGenotyper, and I run 4 pipeline, 3 error

the only correct pipeline:

/Bio/usr/bin/java -Djava.io.tmpdir=./ -jar ./tools/GenomeAnalysisTK.jar -T UnifiedGenotyper -glm BOTH -R ./bol.fa -I ./align/P1.final.bam -I ./align/P2.final.bam -I ./align/R.final.bam -I ./align/S.final.bam -o ./allsnp.vcf
result:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT P1 P2 R S

other 3 error pipeline:

/Bio/usr/bin/java -Djava.io.tmpdir=./ -jar ./tools/GenomeAnalysisTK.jar -T UnifiedGenotyper -glm BOTH -R ./brapa.fa -I ./align/VrP2-1.final.bam -I ./align/VsP1-1.final.bam -I ./VRF2-1.final.bam -I ./align/VSF2-1.final.bam -o ./allsnp.vcf
result:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT VRF2-1 VSF2-1 VrP2-1 VsP1-1

it`s error of order! why does it come?

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @skenoy
    Hi,

    The samples are ordered alphabetically in the output VCF. There is nothing you can do to change it. This is the default so it is easy to keep track of all your samples in an orderly way.

    -Sheila

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