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Old 10-04-2019, 07:51 AM   #1
Marius
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Default Filtering out individual genotype calls with too HIGH read depth from VCF

I have VCF files generated from GATK's HaplotypeCaller. One file per each of 20 individuals. These VCF files will be combined into a multi-sample gVCF for joint genotyping using GenotypeGVCFs (GATK), producing a vcf.gz file including all variable positions across the individuals.

I would like to set a filter to remove certain variants. The tricky part is that this filter is not a global filter, meaning, the filtering threshold should be set differently for each individual. Specifically, I'm looking to exclude any genotype (variant) call *within an individual* that has more than 4-times the average read depth of *that individual*.

How do I achieve such filtering? Can this be done on the combined vcf-file (or even the variants vcf file), or do I have to do such filtering before combining individual VCF files into one?
And, how do I implement this filter? I cannot think of any tool that allows me to filter out positions with a too high read depth, and particularly not if the respective threshold depends on the genome-wide average.

Thank you for your help!
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Old 10-04-2019, 10:59 AM   #2
SNPsaurus
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That would require some scripting, I think. vcftools can filter for sites within a range of read depth, so you could:
extract one individual with vcftools --indv
find the mean depth with vcftools --depth
filter that individual with --max-meanDP

but at that point I would just parse the vcf with a scripting language.
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