How to call denovo variants from multiple trios cohort?
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5 months ago
dare_devil ★ 1.4k

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?

trio denovo gatk germline • 179 views
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Entering edit mode
5 months ago

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

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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?

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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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This format seems correct. You can also go through this link

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