https://bioinformaticsonline.com/snippets/view/41319/install-vcftools-on-ubuntu? https://bioinformaticsonline.com/snippets/view/41319/install-vcftools-on-ubuntu Sun, 01 Mar 2020 23:27:29 -0600 https://bioinformaticsonline.com/snippets/view/41319/install-vcftools-on-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads/annotated$ sudo apt install vcftools [sudo] password for jit: Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: vcftools 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 452 kB of archives. After this operation, 1,459 kB of additional disk space will be used. Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 vcftools amd64 0.1.15-1 [452 kB] Fetched 452 kB in 1s (449 kB/s) Selecting previously unselected package vcftools. (Reading database ... 193392 files and directories currently installed.) Preparing to unpack .../vcftools_0.1.15-1_amd64.deb ... Unpacking vcftools (0.1.15-1) ... Setting up vcftools (0.1.15-1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... #MORE at https://vcftools.github.io/perl_module.html # Calculate stats separately for the filter field, quality and non-indels vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False -p out/ # Calculate stats for all samples vcf-stats file.vcf.gz -f FORMAT/DP=10:200 -p out/ # Calculate stats only for the sample NA00001 vcf-stats file.vcf.gz -f SAMPLE/NA00001/DP=1:200 -p out/ vcf-stats file.vcf.gz > perl.dump]]> Jit