First, you need to use bedtools to convert bam or bed file into bedgraph format for positive strand and negative strand respectively. Please remember multiply the coverage of negative strand by "-1". Then you can merge these two files together and load it in IGV.

Here is the example:

samtools view -h -b Input.bam | bedtools bamtobed -ed -i - | bedtools genomecov -split -strand "+" -i - -g mm10.chrom.sizes -bg -trackline -trackopts 'name="Input" visibility=2 color=255,30,30' > Input.bedgraph
samtools view -h -b Input.bam | bedtools bamtobed -ed -i - | bedtools genomecov -split -strand "-" -i - -g mm10.chrom.sizes -bg | awk '{OFS="\t"}{print $1,$2,$3,$4*-1;}' >> Input.bedgraph

You can't do that in IGV because a coordinate cannot have two different values.

What you can do however is split the data into two tracks and plot the positive values in one and the negative ones in the other