I am trying to merge multiple vcf files using MergeVcfs from Picard tools. Here is my command:
java -jar ./picard.jar I=input1.vcf I=input2.vcf I=inputx.vcf O=combined.vcf
However, I am getting the following error:
Input file .vcf has sample entries that don't match the other files.
This is what I used to call the variants:
gatk HaplotypeCaller -I input.sorted.bam -O .vcf -R reference.fasta
Is this is a problem as I did not output as GVCF? What tool can I use to merge it successfully?