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Genotyping 1000 samples 1000x

grafalgrafal MPI TuebingenMember

Dear GATK specialists,

I would like to ask you for advice; I am genotyping combined gvcf for about 1000 samples. For each of them I have chloroplast genome of about 150kb. Problem is that coverage for those chloroplasts reach 500-1000x. When I try to genotype them altogether - I wait 16h and not even a single position is genotyped for the dataset:

My command:

java -Xmx200G -jar /ebio/abt6/rgutaker/bin/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ref.fa -V combined.gvcf.gz -o genotyped.gvcf -nt 5

Would you have any idea how should I genotype that dataset whilst still being able to include all the information for genotyping?

Many thanks.

Rafal

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