I want to call denovo variants from trios cohort consisiting of 15 trios (15*3 = 45 samples) I followed below mentioned steps:
gatk GenomicsDBImport \
-V data/gvcfs/mother.g.vcf \
-V data/gvcfs/father.g.vcf \
-V data/gvcfs/son.g.vcf \
--genomicsdb-workspace-path trio_db \
--intervals intervals.txt
## Select Variants
gatk SelectVariants \
-R /data/ref/grch38.fasta \
-V gendb://trio_db \
-O trio_selectvariants.g.vcf
## Run joint genotyping on the trio
gatk GenotypeGVCFs \
-R /data/ref/grch38.fasta \
-V trio_db \
-O trioGGVCF.vcf \
-L intervals.txt
Do I need to run this on all the trios individually?
Or
Are there any way to do it?
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DareDevil
run GenomicsDBImport on all your samples.
you don't need to run SelectVariants if you don't select anything....
call the variants with GenotypeGVCFs. Provide a pedigree https://gatk.broadinstitute.org/hc/en-us/articles/360040509751-GenotypeGVCFs#--pedigree and add -A PossibleDeNovo https://gatk.broadinstitute.org/hc/en-us/articles/360040509751-GenotypeGVCFs#--annotation
Hi Pierre Lindenbaum,
Can you guide me to create the pedigree file?. My understanding is a ped file contains following
Family ID Individual ID Paternal ID Maternal ID Sex (1=male; 2=female; other=unknown) Phenotype
Should I make this manually? Or are there other ways to do it?
I created a sample pedigree file as follows:
FamID IndID PatID MatID Sex Phenotype
1 in1 Pat1 Mat1 1 2
1 Pat1 0 0 1 0
1 Mat1 0 0 2 0
2 in2 Pat2 Mat2 1 2
2 Pat2 0 0 1 0
2 Mat2 0 0 2 0
is this the right way to do it? where Pat is fatherID; Mat is MotherID; in is childID
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