Commit 13c61914 authored by Moustakas's avatar Moustakas
Browse files

Improve phrasing and options description

parent 68b4e6d8
# VcfFilter
## Introduction
This tool filters VCF files on a number values. For example, it can filter on sample depth and/or total depth.
It can also filter out the reference calls and/or minimum number of sample passes.
For more on filtering options and how to set them, please refer to the help menu.
This tool enables a user to filter VCF files. For example on sample depth and/or total depth.
It can also be used to filter out the reference calls and/or minimum number of sample passes.
There is a wide set of options which one can use to change the filter settings.
......@@ -32,19 +37,19 @@ Usage: VcfFilter [options]
Min number of samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth
--minBamAlternateDepth <int>
--denovoInSample <sample>
Only show variants that contain unique alleles in compete set for given sample
Only keep variants that contain unique alleles in complete set for the given sample
--mustHaveVariant <sample>
Given sample must have 1 alternative allele
Only keep variants that for the given sample have an alternative allele
--diffGenotype <sample:sample>
Given samples must have a different genotype
--filterHetVarToHomVar <sample:sample>
If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filtered
Only keep variands that for the given samples have a different genotype
--filterHetVarToHomVar <sample1:sample2>
Filter out varianst that are heterozygous in sample1 and homozygous in sample2
--filterRefCalls
Filter when there are only ref calls
Filter out ref calls
--filterNoCalls
Filter when there are only no calls
Filter out no calls
--minQualScore <value>
Min qual score
Filter out variants with Min qual score below threshold
~~~
To run the tool:
......@@ -54,4 +59,4 @@ biopet tool VcfFilter --inputVcf myInput.vcf \
~~~
## Output
The output is a vcf file containing the filters specified values.
\ No newline at end of file
The output is a vcf file containing the values that pass the user-defined filtering options
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