Question: Can GATK work directly on read and quality score data
gravatar for devinliao0918
5.7 years ago by
United States
devinliao091830 wrote:

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




next-gen • 1.4k views
ADD COMMENTlink written 5.7 years ago by devinliao091830

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

ADD REPLYlink written 5.7 years ago by geek_y11k

Thanks for your suggestions.

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

ADD REPLYlink written 5.7 years ago by devinliao091830
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