I have encountered an issue with FreeBayes in the multibam version. If the samples were sequenced sequentially on the same chip and machine, I obtain a VCF with calls for all the samples present in the multibam. However, if the samples were sequenced sequentially on different chips and machines, FreeBayes only provides calls for one of the samples in the VCF.
freebayes --bam-list bamfilelist.txt --fasta-reference UCSC/hg19.fa --report-all-haplotype-alleles -@ panel_paternitanoninvasiva.sort.vcf.gz -i -X -u --legacy-gls --min-repeat-entropy 0 --use-best-n-alleles 4 --target IAD217514_151_Designed.bed > samples.vcf