Pre-processing the data from 10xchromium

[llBencchll]

Hello,

I am now struggling to generate the base quality score table for the bam file generated from cellranger pipeline. As the cellranger mapped the sequencing file to grch38 genome, the vcf file from gatk resource bundle is not compatible. While the vcf files from 1000 genome project are doable, they are splited into different chromosome and each file take up a bit of storage place. Is there any suggestion to get around with this problem or if there's any way to merge the base quality score table generated for each chromosome into one?