How do I call compound hetrozygosity from multiple trios cohort?
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5 weeks ago
dare_devil ★ 1.4k

I have a cohort of 15 trios comined as a vcf file. It contains 15x3 (45 sample) vcf information

gatk CombineGVCFs \
    -R $reference \
    -L $interval \
    --variant 001C1.vcf.gz \
    --variant 001c2.vcf.gz \
    --variant 001P1.vcf.gz \
        .....
        .....
        -O cohort.g.vcf.gz

gatk --java-options "-Xmx16g" GenotypeGVCFs  --reference $reference --variant cohort.g.vcf.gz --output output.vcf.gz --dbsnp $DBSNP --intervals $interval

and I have the pedigree info for the family as:

#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

How can I now identify the compound heterozygosity from the cohort for the affected samples for each family ? Any help appreciated.

ped gatk trio heterozygosity compound vcf • 145 views
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use gatk VariantAnnotator -A PossibleDeNovo --pedigree input.ped ....

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I performed this step also, but how do I find out compound hetrozyosity from the output file.

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