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Invariant Reference-like sites have lower quality scores?
It seems invariant sites that have the Reference allele get much lower quality scores than contiguous, polymorphic sites with the same coverage. Also, perhaps because of the quality issue, these homozygous genotypes at the reference-like invariant site aren't given likelihood scores (PL field). Is there a way to get the GATK to output likelihoods for homozygous genotypes at these sites? Thanks!
I used the following command to use the GATK:
bsub -q bigmem -o Bridip -n 48 -R "span[ptile=48]" java -Xmx48g -jar /n/sw/GenomeAnalysisTK-2.3-4-g57ea19f/GenomeAnalysisTK.jar -R alyrata.nuc.org.fa -T UnifiedGenotyper -I ALL_SAMPLES.realigned.bam -glm SNP -stand_call_conf 50.0 -stand_emit_conf 10.0 --output_mode EMIT_ALL_SITES -o LeviIsRaddip.vcf