Hi everyone!
My goal is to run VQSR on VCFs generated with samtools mpileup.
According to GATK best practices first i have to run VariantAnnotator on each of my VCFs in order to do that.
here's the annotation options I included in the command line:
--annotation QualByDepth
--annotation RMSMappingQuality
--annotation MappingQualityRankSumTest
--annotation ReadPosRankSumTest
--annotation FisherStrand
--annotation StrandOddsRatio
--annotation DepthPerSampleHC
--annotation InbreedingCoeff
unfortunately it returns these warnings:
WARN 17:26:07,297 StrandBiasTest - No StrandBiasBySample annotation or read data was found. Strand bias annotations will not be output.
WARN 17:26:07,297 InbreedingCoeff - Annotation will not be calculated. InbreedingCoeff requires at least 10 unrelated samples.
WARN 17:26:07,297 StrandBiasTest - No StrandBiasBySample annotation or read data was found. Strand bias annotations will not be output.
WARN 17:29:25,076 AnnotationUtils - DP annotation will not be calculated, must be called from HaplotypeCaller or MuTect2, not VariantAnnotator
I don't care about DP as for WXS it is not required, but the others are mandatory for VQSR (right?)
I'm using samtools to generate VCF for a couple of reasons: i need to call variants from single samples, i need a tool that calls "everything" without filters in order to apply custom downstream filtering. the idea is to try first the VQSR approach for the artifact filtering instead of hardfiltering (which is more tricky and complex).
I was thinking about using Haplotype Caller (also because it would be easier to use HC VCFs with VQSR or other GATK tools), but for what I have understood it is meant to find "germline SNPs", which doesn't fit my needs as I am looking for novel SNV (mutations) and not SNPs (am I right?).
Thank you very much.