comparison vcffilter.xml @ 2:77e44d465705 draft

Uploaded

1:e5dd21db760b

    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
    -A, --append-filter   append the existing filter tag, don't just replace it
    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
    -v, --invert          inverts the filter, e.g. grep -v
    -o, --or              use logical OR instead of AND to combine filters

Filters are specified in the form {ID}  {operator} {value}::

 -f "DP > 10"  # for info fields
 -g "GT = 1|1" # for genotype fields
 -f "CpG"  # for 'flag' fields

Operators can be any of: =, !, <, >, pipe, &

Any number of filters may be specified.  They are combined via logical AND
unless --or is specified on the command line.

For convenience, you can specify "QUAL" to refer to the quality of the site, even
though it does not appear in the INFO fields.

</help>
</tool>

2:77e44d465705

    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
    -A, --append-filter   append the existing filter tag, don't just replace it
    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
    -v, --invert          inverts the filter, e.g. grep -v
    -o, --or              use logical OR instead of AND to combine filters
    -r, --region          specify a region on which to target the filtering (must be used in conjunction with -f or -g

Filters are specified in the form {ID}  {operator} {value}::

 -f "DP > 10"          # for info fields
 -g "GT = 1|1"         # for genotype fields
 -f "CpG"              # for 'flag' fields

Any number of filters may be specified.  They are combined via logical AND unless --or is specified on the command line. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.  

Operators can be any of: =, !, <, >, pipe, &


To restrict output to a specific location use -r option (much be used in conjunction with -g or -f)::

 -r chr20:14000-15000  # only output calls between positions 14,000 and 15,000 on chromosome 20
 -r chrX               # only output call on chromosome X

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Vcffilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).

</help>
</tool>