# Hard Filter Bash
By Tanya Lama

############################################
### Select variants by excluding nonvariants
############################################

java -Xmx$MEM -jar ${GATK} \
-R ${REFERENCE} \
-T SelectVariants \
--excludeNonVariants \
-V ${inDir}/5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
-o ${outDir}/${Chrom}/1_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

###############
### Hard filter
###############

1a_SV_5GS_5TM_joint_chr_HighQualSites_processed.vcf.gz
java -Xmx16G -jar ${GATK} \
-R ${REFERENCE} \
-T VariantFiltration \
-nt 24\
-V ${outDir}/${Chrom}/1_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
-filter "QD < 2.0" -filterName "lowQD" \
-filter "FS > 60.0" -filterName "highFS" \
-filter "MQ < 40.0" -filterName "lowMQ" \
-filter "MQRankSum < -12.5" -filterName "lowMQRankSum" \
-filter "ReadPosRankSum < -8.0" -filterName "lowReadPosRankSum" \
-o ${outDir}/${Chrom}/2_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

###################################################################################################
###### Select variants
###### The goal of this intermediate file is to quickly check whether GATK is doing the right thing
###################################################################################################

java -Xmx$MEM -jar ${GATK} \
-R ${REFERENCE} \
-T SelectVariants \
-V ${outDir}/${Chrom}/2_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
-ef \
-o ${outDir}/${Chrom}/3_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

###################################################
###### Select variants
###### Select biallelic SNP
###### Only retain sites that are annotated as PASS
###################################################

java -Xmx$MEM -jar ${GATK} \
-R ${REFERENCE} \
-T SelectVariants \
-V ${outDir}/${Chrom}/3_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
-selectType SNP \
--restrictAllelesTo BIALLELIC \
-o ${outDir}/${Chrom}/4_BiSNP_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

##################################################
###### Remove clustered SNPs (> 3SNPs within 10bp)
##################################################

java -Xmx$MEM -jar ${GATK} \
-R ${REFERENCE} \
-T VariantFiltration \
-V ${outDir}/${Chrom}/4_BiSNP_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
--clusterWindowSize 10 --clusterSize 3 \
-o ${outDir}/${Chrom}/5_rmClusterSNP_BiSNP_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

########################
###### Retain PASS sites
########################

java -Xmx$MEM -jar ${GATK} \
-R ${REFERENCE} \
-T SelectVariants \
-V ${outDir}/${Chrom}/5_rmClusterSNP_BiSNP_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz \
-ef \
-o ${outDir}/${Chrom}/6_SV_rmClusterSNP_BiSNP_SV_HardFilter_SV_5GS_5TM_joint_${Chrom}_HighQualSites_processed.vcf.gz

###### tags: `tools`