the_script_VCF_count_mutations.sh

#!/bin/bash

## the bash script reads the gender (MALE, FEMALE), the NORMAL and the TUMOR files (BAM), and the CHROMOSOME to run the analysis on.

PICARD="java -jar /N/users/btanasa/Software/picard-tools-1.140/picard.jar"
SAMTOOLS="samtools"
GATK="java -Xmx8g -jar /N/users/btanasa/GATK-3.5/GenomeAnalysisTK.jar"
MUTECT1="java -Xmx8g -jar /N/users/btanasa/Software/mutect-1.1.7/mutect-1.1.7.jar" 

DBSNP138="/N/projects/spcg/subjects/resources/Homo_sapiens_assembly38.dbsnp138.vcf"
COSMIC76="/N/projects/spcg/subjects/resources/COSMIC76-coding-and-noncoding.21march2016.vcf"

REFERENCE_HG38_MALE="/N/projects/spcg/subjects/resources/genomeM.fa"
REFERENCE_HG38_FEMALE="/N/projects/spcg/subjects/resources/genomeF.fa"

### to merge the VCF files containing SNVS and INDELS  

FILE=$1


if [ "$GENDER" == "MALE" ]; then  
   REFERENCE=$REFERENCE_HG38_MALE
fi

if [ "$GENDER" == "FEMALE" ]; then 
   REFERENCE=$REFERENCE_HG38_FEMALE
fi 

echo "do list the total number of MUTATIONS"

grep "#" -v $FILE | wc -l 

echo "do list the total number of SNVS"

grep "=SNP"  $FILE | wc -l 

echo "do list the total number of INSERTIONS"

grep "=INSERTION" $FILE | wc -l 

echo "do list the total number of DELETIONS"

grep "=DELETION" $FILE | wc -l