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GenotypeGVCFS gives fewer samples than input.
I ran GenotypeGVCFs with the following command
java -Xmx$64g -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R --variant 08_22_2016_murat5.list --dbsnp dbsnp_144.hg38.vcf.gz -o murat5_08_22_2016_raw.vcf -log murat5_08_22_2016_raw.log -L MedExome_hg38_capture_targets.bed -nt 1 --max_alternate_alleles 6
The list I am inputting into --variant contains the paths to 397 gvcfs. When I run vcftools --vcf murat5_08_22_2016_raw.vcf I get the output:
VCFtools - v0.1.12b
(C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted:
After filtering, kept 380 out of 380 Individuals
After filtering, kept 397293 out of a possible 397293 Sites
Run Time = 95.00 seconds
Is there any reason why 17 samples are thrown out?
Thank you very much.