Commit 7e3e31cb authored by Moustakas's avatar Moustakas
Browse files

Improved Documentation

parent c872ae76
# CheckAllelesVcfInBam
## Introduction
This tool has been written to check the allele frequency in BAM files.
This tool has been written to check the allele frequency in BAM files. This is meant for comparison with the allele frequency reported at the VCF file
## Example
To get the help menu:
......@@ -16,14 +16,15 @@ Usage: CheckAllelesVcfInBam [options]
-v | --version
Print version
-I <file> | --inputFile <file>
VCF file
-o <file> | --outputFile <file>
output VCF file name
-s <value> | --sample <value>
sample name
-b <value> | --bam <value>
bam file, from which the variants (VCF files) were called
-m <value> | --min_mapping_quality <value>
minimum mapping quality score for a read to be taken into account
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To run the tool:
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