How can I creating multisample VCF file ?

Question

[eennadi]

Hello,

I want to create a multisample VCF file. I have bam files from various alignment.

I ran the command

bcftools mpileup -d 100000 -f  ~reference  *.bam | bcftools call -c  > concate.vcf

Is this step scientifically correct? Or do I need to merge all bam first before running the above command?

Thanks

[Pierre Lindenbaum]

Is this step scientifically correct?

yes , althought most people use -m , not -c http://www.htslib.org/workflow/wgs-call.html

   -c, --consensus-caller          The original calling method (conflicts with -m)
   -m, --multiallelic-caller       Alternative model for multiallelic and rare-variant calling (conflicts with -c)