Jit
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Install vcftools on Ubuntu
By Jit 1728 days ago
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
