Are there "canonical" quality score cutoffs for GATK vcf outputs that are more or less standard in the literature? Many papers don't report their cutoffs more mutation calls, values that I've seen include >40 or 50 for read quality (GATK's default) and >20 for GQ (genotype quality scores). The latter seems far too conservative, at least in view of the number of mutations I'm finding per sample vs. those reported for similar tumor samples in the literature.
•
written
by
Max
1 answer
GATK should add LowQuality flags in the .vcf.
At least for the examples I have seen, the high quality results (labeled with a ".", instead of "HighQuality") should be pretty safe calls and I would just use either the full .vcf or focus on the variants without the "LowQuality" flag.
Log in to answer this question.
-
What is the set of all possible GT calls for a VCF or gVCF for human data.
written by ariel
-
Variant quality scores with different variant caller: HaplotypeCaller vs DeepVariant. How to interp…
written by Jordi •
-
Somatic variant calling with/without matched normal sample (Mutect2)
written by newbio17
-
varscan2 somatic sip
written by fabbri.marco •
-
Quality scores in ICGC simple somatic mutation file
written by tralynca •
-
Can We Call Variants Based On Alt Allele Frequncy?
written by ivivek_ngs
-
Next-Generation Sequecing And Quantitative Traits Association Study
written by sorento7 •
-
Variant Effect Predictor On Domain Level
written by jackuser1979
-
Filtering Variant Calls Based On Genotype Quality
written by Kssr
-
Comparison Of Two Versions Of Gatk Filtering For Exome Sequencing Data.
written by michealsmith
