I have 2 sorted Bam files and I want to merge them and get a VCF file from them using samtools pileup.
first i merge these 2 files with
samtools merge and then I get a VCF file as output.
samtools mpileup genome.fa merged-bam.bam output.vcf
then I use
samtools mpileup genome.fa 1.bam 2.bam output.vcf
but the output of these 2 approach had different size. where am I doing wrong?
thanks a lot