Can GATK work directly on read and quality score data
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
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devinliao0918 •
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you can use, STACKS or pyRAD for genotyping from fastq files.
Thanks for your suggestions.
I actually hope to see how the genotype-calling algorithm works in GATK.