CheckAllelesVcfInBam

Introduction

This tool has been written to check the allele frequency in BAM files.

Example

To get the help menu:

java -jar Biopet-0.2.0.jar 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>

  -o <file> | --outputFile <file>

  -s <value> | --sample <value>

  -b <value> | --bam <value>

  -m <value> | --min_mapping_quality <value>

To run the tool:

java -jar Biopet-0.2.0.jar 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:

java -jar Biopet-0.2.0.jar 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.