Joint variation calling

variantCall.sh

## Variant call

## Input files
gatk_jar=gatk3.jar # https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk/?pli=1
refseq=genome.fa
rmdupN=normal.bam  ## aligned & duplication removed bam file
rmdupP1=primary1.bam
rmdupP2=primary2.bam
rmdupM1=metastasis1.bam
rmdupM2=metastasis2.bam
# rmdupM3=metastasis3.bam  ## You can add more files
vcf_raw=output.vcf

## Run the joint Variant Calling
java -Xmx70G -jar $gatk_jar -T UnifiedGenotyper \
-nt 10 \
-R $refseq \
-I $rmdupN \ ## Normal
-I $rmdupP1 \ ## Primary1
-I $rmdupP2 \ ## Primary2
-I $rmdupM1 \ ## Metastasis1
-I $rmdupM2 \ ## Metastasis2
-o $vcf_raw \
-glm BOTH \
--min_base_quality_score 15 \
--min_indel_count_for_genotyping 2 \
--min_indel_fraction_per_sample 0.05 \
--output_mode EMIT_VARIANTS_ONLY \
--sample_ploidy 2 \
--standard_min_confidence_threshold_for_calling 10.0 \
--standard_min_confidence_threshold_for_emitting 10.0