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Reference confidence model for processing multiple samples with low coverage
I am using the Reference confidence model for processing multiple samples with low coverage. Is there a way of specifying a minimum and a maximum depth per read? My script looks like this:
java -jar $gatk_dir/GenomeAnalysisTK.jar -T HaplotypeCaller -R ref_loci.fa -I $i."sorted.bam" -stand_call_conf 30 -stand_emit_conf 5 -o ./$i".g.vcf" -ERC GVCF --variant_index_type LINEAR --variant_index_parameter 128000
I included the -stand_call_conf and the -stand_emit_conf, but it doesn't look like it makes a difference with or without those parameters. Is there another way of specifying depth range?