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.
questions about downsampling
Hi, I am using HaplotypeCaller to call variants on targer region sequencing data, the mean coverage is about 600, I want to downsample my data to test the minumum mean coverage required for variant calling.So I use the parameter -dcov, the script is pasted below:
-T HaplotypeCaller -A StrandAlleleCountsBySample -L target_region.bed -R hg19.fasta -I sample.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -dcov 100 -o sample.vcf
However, error message appears:
ERROR MESSAGE: Invalid command line: Cannot use -dcov or --downsample_to_coverage for ActiveRegionWalkers, use another downsampling argument
How can I solve the problem? Thanks a lot!