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