diff --git a/docs/tools/VcfFilter.md b/docs/tools/VcfFilter.md index c9b3f064700c74181489097aaebfc6085dc8497e..1335e9b94a9f06790bf807b11a8e971ae8363fb3 100644 --- a/docs/tools/VcfFilter.md +++ b/docs/tools/VcfFilter.md @@ -1,6 +1,11 @@ # 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