GATK_diploid.bsh

cd mapped/bam/sorted/readgrouped
for file in *.bam
do
	#java -jar ../../../../../GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R ../../../../../Dotse1_AssemblyScaffolds_Repeatmasked.fasta --sample_ploidy 2 -ERC GVCF -I $file -o ${file}.diploid.g.vcf
	java -jar ../../../../../GATK/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ../../../../../Dotse1_AssemblyScaffolds_Repeatmasked.fasta -V ${file}.diploid.g.vcf -o ${file}.diploid.vcf
done
#for file in *.diploid.vcf
#do
	#java -jar ../../../../../GATK/GenomeAnalysisTK.jar -T VariantFiltration -R ../../../../../Dotse1_AssemblyScaffolds_Repeatmasked.fasta -V $file --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0" --filterName "my_snp_filter" -o ${file}.filtered.vcf
#Q20 filter
	#java -jar ../../../../../GATK/GenomeAnalysisTK.jar -T VariantFiltration -R ../../../../../Dotse1_AssemblyScaffolds_Repeatmasked.fasta -V ${file}.filtered.vcf -G_filter "GQ < 20.0" -G_filterName lowGQ -o ${file}.Q20.vcf  
#done