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CombineGVCFs

mahyarheymahyarhey BostonMember

Hi,
I used the following commands to combine all my 33 VCF files. There is no error in log file and the program create an output. But, when I checked the output, all geneotypes are (./.) and there is no 0/0 or 0/1 or 1/1. This is absolutely strange. what is wrong? please advise

java -jar /gatk-3.3-0/gatk/GenomeAnalysisTK.jar \
-R ucsc.hg19.fasta \
-T CombineGVCFs \
--variant sample1 \
--variant sample2 \
--variant sample3 \
..
..
--variant sample33 \
--out Combined_all33VCF.vcf

Could you please let me know what is wrong and why I have not any call in my output. All geneotypes are (./.)??????????????

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