Can GATK work directly on read and quality score data

Question

[devinliao0918]

Typically, we use GATK to call variants if the Bam files are available. However, now I only have read and quality scores data for several loci, but I would like to use GATK or Samtools to call the genotypes. Is it feasible? My data looks like

                                  Variant 1
Subject 1        AAAAACCC    HHHGGGFT (base quality score)   
Subject 2        AAAAC       HFFB@
Subject 3        CCCCCCC     DG?F@BB
.
.
.

[GouthamAtla]

you can use, STACKS or pyRAD for genotyping from fastq files.

[devinliao0918]

Thanks for your suggestions.

I actually hope to see how the genotype-calling algorithm works in GATK.