Order of the sample names in cohort VCF file using GenotypeGVCFs
I wanted to produce the cohort vcf file from several g.vcf files made using HaplotypeCaller. I used the 'GenotypeGVCFs' and gave a list of g.vcf files. The order of samples in the final vcf file is different from the gvcf file list I provided. It looks like it sorted alphabetically with the sample name. How can I get samples in the same order as in the gvcf file list? I am using GATK 3.3.