I had done
- Sorting sam file
- Mark duplicates
- Realignment call variants
- Call raw snps and Apply hard filtering
Then I merge my three vcf files (dad, mum, child)
java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg38.fa --variant sample02.vcf --variant sample06.vcf --variant sample08.vcf -o 268merged.vcf -genotypeMergeOptions UNIQUIFY
and apply next genotype refinement workflow
Im wondering if its common to dont get any results as hiConfDeNovo and lowConfDeNovo in the results (raw snps or after hard filtering)
INFO=<ID=hiConfDeNovo,Number=1,Type=String,Description="High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]"> INFO=<ID=loConfDeNovo,Number=1,Type=String,Description="Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]"> CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample02.variant sample06.variant2 sample08.variant3 1 917495 . C T 30.74 PASS AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;PG=0,0,0;QD=15.37;SOR=0.693;set=variant3 GT:AD:DP:FT:GQ:PL:PP ./.:.:.:PASS ./.:.:.:PASS 1/1:0,2:2:lowGQ:6:58,6,0:58,6,0
Its possible. But I think following change would help.
SelectVariantsand perform hard filtration
Can you confirm that following steps were followed after hard filtration?
CalculateGenotypePosteriors. A ped file will have to be provided.
-A PossibleDeNovooption. Again ped file will have to be provided.