Hello, I'm wondering if it's possible to calculate FQ scores, such as those found in a vcf file generated using samtools/bcftools mpileup, from information in a GATK(4.2) vcf.
Are GQ/QUAL for the variant sites and RGQ for the invariant sites convertible to FQ score (or an approximate FQ-like score)?
For context, I'd like to convert a GATK all-sites vcf file to a diploid fastq file (using vcfutils.pl vcf2fq). This command runs fine on the variant sites in a GATK all sites vcf but replaces all the invariant sites in the fastq output with "n" as vcf2fq requires an FQ score. Or is there an alternate way to generate a diploid fastq sequence using a GATK all sites vcf?
Some background on FQ score from the samtools documentation: "FQ Consensus quality. If positive, FQ equals the phred-scaled probability of there being two or more different alleles. If negative, FQ equals the minus phred-scaled probability of all chromosomes being identical. Notably, given one sample, FQ is positive at hets and negative at homs."
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