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CombineGVCFs: After combining 3 GVCF file, some information has losed.

Hi,
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-4.0.2.1/gatk-package-4.0.2.1-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.

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @erya
    Hi,

    What happens after you run GenotypeGVCFs on the output of CombineGVCFs? CombineGVCFs output is not the final VCF that should be used in analysis.

    -Sheila

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