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.
DP and chromosome filtering
This is two separate questions:
Starting with a vcf file, plotting the depth (DP) distribution gives a nice, slightly asymmetrical bell-shaped curve. Given that SNPs with very high and very low coverages should be excluded, how does one decide what is very high and low. e.g. 5% either side ?
I'm only interested in chromosomes 2L, 2R, 3L, 3R and X of my Drosophila sequences. Filtering for these is easy with a Perl script but I'm trying to do this earlier on in the GATK processes. I've tried ...-L 2L -L 2R -L 3L ...etc, -L 2L 2R 3L ....etc and, -L 2L, 2R, 3R...etc but the result is either input error message or chromosome 2L only.
Many thanks and apologies if I've missed anything in the instructions.