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CombineGVCFs: After combining 3 GVCF file, some information has losed.
When I used GATK4.0 CombineGVCFs to combine 3-sample GVCF file into a multi-sample GVCF file, a lot of information didn't preasent.
As the three pictures present, the size of every file is greater than 1.0GB,
After combining, the size of the file is just 10.7KB.
My command is:
java -jar /home/wang/Documents/gatk-220.127.116.11/gatk-package-18.104.22.168-local.jar CombineGVCFs -R /mnt/hgfs/D/analysis/populus/populus.fasta -V p1_output_raw_snps_indels.g.vcf -V p2_output_raw_snps_indels.g.vcf -V p3_output_raw_snps_indels.g.vcf -O p_output_raw_snps.g.vcf
So I want to know what caused this problem and how to solve it.