If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
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.
I have problem with Hard Filtering, anyone to help?
Hi guys, I was trying to run the below command and I got an invalid error from my argument. I could not find any mistake in my command and have also regenerated my input raw SNPs file but error remain the same. I could not also find any thread that have addressed this problem. What do you think I am doing wrong? logfile=filtered.error gatk 3.7.0 \ -T VariantFiltration \ -R fasta.fa \ -V raw_SNPs.vcf.gz \ --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" \ --filterName "default_SNP_filter" \ -o filtered_SNPs.vcf \ 2> >(tee "$logfile")
ERROR Invalid argument value '2.0' at position 9. ERROR Invalid argument value '||' at position 10. ERROR Invalid argument value 'FS' at position 11. ERROR Invalid argument value '>' at position 12. ERROR Invalid argument value '60.0' at position 13. ERROR Invalid argument value '||' at position 14. etc..