change hardfiltering parameter

Snakemake/IMAGE_vqsr/rules/hardfiltering.smk

@@ -18,7 +18,7 @@ rule VariantFiltration:
     params:
         mem= config["VariantFiltration"]["mem"],
         filter_name = "\"{var}_HardFiltered\"",
-        filter_exp = lambda wildcards : "\"QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0\"" if wildcards.var=="SNP" else "\"QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0\""
+        filter_exp = lambda wildcards : "\"QD < 2.0; MQ < 40.0; FS > 60.0; SOR > 3.0; MQRankSum < -12.5; ReadPosRankSum < -8.0\"" if wildcards.var=="SNP" else "\"QD < 2.0; ReadPosRankSum < -20.0; InbreedingCoeff < -0.8; FS > 200.0; SOR > 10.0\""
     shell:
         """
         java -Xmx{params.mem} -jar {config[bin][gatk]} -T VariantFiltration -R {input.ref} -V {input.vcf} --filterName {params.filter_name} --filterExpression {params.filter_exp} -o {output.vcf} 2> {log}