Using qctool in a pipeline
Outputting data to stdout
Using "-" as an output file specifier will output data to standard output, that can then be redirected
or piped into other commands. For example:
$ qctool -g example.bgen -og -
This outputs genotype data to stdout.
(By default output is in VCF format; use the
-ofiletype
option to alter this).
$ qctool -g example.bgen -snp-stats -osnp -
This outputs SNP summary statistics to standard output.
Inputting data from stdin
QCTOOL has limited support for reading data from stdin.
To do this, specify "-" as the argument to
-g
, and specify the format of the input data
using the -filetype
option, e.g.:
$ cat file.bgen | qctool -g - -filetype bgen [other options]
This functionality is currently limited to input data in BGEN format (-filetype bgen
)
or in VCF format (-filetype vcf
). VCF format data should be streamed uncompressed, e.g.:
$ cat file.vcf.gz | gunzip -c | qctool -g - -filetype vcf [other options]
Pipelining QCTOOL with other tools
As an example, the following command uses bgenix with QCTOOL to
compute snp summary statistics from a subset of a BGEN file, and view the result on the fly using
less
.
$ bgenix -g file.bgen -range 11:3500000-6500000 | qctool -g - -filetype bgen -snp-stats -osnp - | less -S