CheckAllelesVcfInBam.md

CheckAllelesVcfInBam

Introduction

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:

biopet tool CheckAllelesVcfInBam -h
Usage: CheckAllelesVcfInBam [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -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

To run the tool:

biopet tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
--bam myBam1.bam --sample bam_sample1 --outputFile myAlleles.vcf

Note that the tool can run multiple BAM files at once. The only thing one needs to make sure off is matching the --bam and --sample in that same order.

For multiple bam files:

biopet tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
--bam myBam1.bam --sample bam_sample1 --bam myBam2.bam --sample bam_sample2 \
--bam myBam3.bam --sample bam_sample3 --outputFile myAlleles.vcf

Output

outputFile = VCF file which contains an extra field with the allele frequencies per sample given to the tool.