Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?