If I read a valid vcf with the last 3.8 Bioconductor version 1.28.1

param_T <- ScanVcfParam(sample = samples_names[1],  geno = c("AD", "MQ", "DP", "AF"), info = c("DP","AF", "CALLERS"))
  Tumor <- readVcf(file = vcf_file[i], genome = "GRCH37", param = param_T)
  

head of  vcf_file[i
##fileformat=VCFv4.2
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>

and then I save it with 

writeVcf(Tumor, paste0("./vcf/",samples_names[1], ".vcf"), index = F)

the header is out of order ##fileformat=VCFv4.2 is not on the first line and there is a Strange SAMPLE field 

Thanks for you support!

##SAMPLE=Tumor
##commandline="/home/pastore/data/bcbio/anaconda/bin/freebayes -f /lila/data/abdelwao-lab/pastorea/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --genotype-qualities --strict-vcf --ploidy 2 --targets /lila/data/abdelwao-lab/pastorea/Project/Ben/histiocytosis/hempact/work/freebayes/1/B02_816_T1-1_0_249250621-regions-nolcr.bed --min-repeat-entropy 1 --no-partial-observations --min-alternate-fraction 0.05 --pooled-discrete --pooled-continuous --report-genotype-likelihood-max --allele-balance-priors-off /lila/data/abdelwao-lab/pastorea/Project/Ben/histiocytosis/hempact/work/align/C_K0Y3K8_T001_d/C_K0Y3K8_T001_d-sort.bam /lila/data/abdelwao-lab/pastorea/Project/Ben/histiocytosis/hempact/work/align/PON/PON-sort.bam"
##fileDate=20181115
##fileformat=VCFv4.2
##phasing=none

Thanks for reporting the inconsistent ordering of the header lines in writeVcf(). I've checked in a fix to VariantAnnotation 1.28.2 and 1.29.1 to enforce 'fileformat' as the first line.

As for the SAMPLE line in the header, this must be a carry over from your original file, e.g.,

header(scanVcfHeader(file))

If this is not the case, please send me the vcf file (valerie.obenchain@roswellpark.org) so I can try to reproduce this.

Valerie