Hi, all. Recently I tried Pilon wishing to get the fixed vcf and the sequences. But there are many samples, each of which was sequenced in two lanes. I've run Pilon with commands like below

For one sample:
java -Xmx10G -jar pilon-xx.jar --genome ref.fa --bam A_L1.bam --bam A_L2.bam --output pilon.1 --outdir ./ --vcf --fix all,breaks --threads 20 --minmq 30 --minqual 30

For two samples: java -Xmx10G -jar pilon-xx.jar --genome ref.fa --bam A_L1.bam --bam A_L2.bam --bam B_L1.bam --bam B_L2.bam --output pilon.1 --outdir ./ --vcf --fix all,breaks --threads 20 --minmq 30 --minqual 30

But the output was similar that there is only one column for SAMPLE. I wonder is Pilon couldn't verify those group tags in the bam files like samtools? Besides, I got one prefix.fasta file apart from the vcf file. Is that the corresponding sequence of the sample?

I've searched the community and found one closed question. So I hope someone familiar with Pilon could help me with that. Thanks in advance.