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BeagleOutputToVCF Error "Unable to read index file, for input source: .r2"
dear GATK team,
i am trying to convert beagle output files back to vcf format.
but i always get the following error:
ERROR MESSAGE: Unable to read index file, for input source: /Chr25.r2.idx
i have tried it with GATK 2.6-4 and 2.8.1.
my code is as follows:
java -Xmx4g -jar $GATKDir2/GenomeAnalysisTK.jar \
-R $refDir/$reference \
-T BeagleOutputToVCF \
-l INFO \
-V $vcfDir/Chr25-Raw.vcf \
-beaglePhased:BEAGLE $beagleDir/Chr25.phased \
-beagleProbs:BEAGLE $beagleDir/Chr25.gprobs \
-beagleR2:BEAGLE $beagleDir/Chr25.r2 \
i tried to index the .r2 file with igvtools
java -Xmx4g -jar $igvDir/igvtools.jar index $beagleDir/Chr25.r2
but that does not recognize the file type.
Unknown File Type
i also tried with an "empty" vcf like this;
pseudoVCF to run beagleToVCF
CHROM POS ID REF ALT QUAL FILTER INFO
any help highly appreciated!
best regards marlies