vcf-stats - statistic of VCF file
vcf-stats [OPTIONS] file.vcf.gz
- -d, --dump
<file>
- Take an existing dump file and recreate the files (works with
-p)
- -f, --filters
<filter1,filter2>
- List of filters such as column/field (any value), column/field=bin:max
(cluster in bins),column/field=value (exact value)
- -p, --prefix
<dir/string>
- Prefix of output files. If slashes are present, directories will be
created.
- -s, --samples
<list>
- Process only the listed samples, - for none. Excluding unwanted samples
may increase performance considerably.
- -h, -?,
--help
- This help message.
- # 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