<![CDATA[BOL: Convert VCF to tab-deilimited table]]> https://bioinformaticsonline.com/pages/view/36624/convert-vcf-to-tab-deilimited-table? https://bioinformaticsonline.com/pages/view/36624/convert-vcf-to-tab-deilimited-table Tue, 15 May 2018 07:39:08 -0500 https://bioinformaticsonline.com/pages/view/36624/convert-vcf-to-tab-deilimited-table <![CDATA[Convert VCF to tab-deilimited table]]> Performed with GATK :

java -Xmx8g -jar GenomeAnalysisTK.jar \
-T VariantsToTable \
-R reference.fa \
-V reference_genomes_GT.vcf \
-F CHROM -F POS -F REF -F ALT -GF GT \
-o reference_genomes_GT.table
multiple_sample.vcf should also be converted to multiple_sample_GT.table using this approach.

]]> Seema Singh