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vcf file generated using HaplotypeCaller does not contain dat lines
I typed the following command for finding snps and indels:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R chr21/chr21.fa -I chr21/alignments/human38chr21.sorted.bam -o chr21/humanoutput.raw.snps.indels.vcf
I even got the vcf file but it contains only the header and does not contain the data lines.What maybe wrong?
I hae attached the file containing the stack trace.