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Filtering VCF file to remove ./.

Hello,
I am trying to understand my sample format in my merged vcf file of RNA-seq SNPs produced from the GATK best practices. I have several vcf files that I have merged into one file using combinevariants. Before the files are merged, the format of each sample is mostly 1/1 and 0/1. I understand what these genotypes mean, but after I merge the files, I end up with lots of SNPs that have the genotype "./." while one of the other samples has1/1. I have been reading through other people's work and it seems like maybe "./" indicates that this SNP did not have a high enough quality for this sample? I want to select from my merged vcf file only those variants that pass the quality for all individual files. Just to clarify, if I had three vcf files merged and one variant in these files had the genotype 1/1, 1/0, and 0/0 respectively, I want to keep that variant. However, if there was a variant with the genotypes 1/1, 1/0, and ./., I don't want to keep that variant. Am I understanding what ./. means correctly? And is there an easy way to remove these variants from my merged file? Thank you very much for your help!
Leigh Ann

Answers

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