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.
SplitNCigar with draft assembly?
Hi, I'm trying to use the RNAseq best practices to call SNPs in transcriptomes aligned to a draft assembly for a non-model species. Everything has worked fine so far, but when I try to use SplitNCigar it doesn't seem to filter anything:
INFO 14:09:51,596 ProgressMeter - Total runtime 961.86 secs, 16.03 min, 0.27 hours
INFO 14:09:51,598 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 21140216 total reads (0.00%)
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 14:09:51,599 MicroScheduler - -> 0 reads (0.00% of total) failing ReassignOneMappingQualityFilter
Done. There were no warn messages.
Is this because my genome lacks annotations? Is there a way to use the splice junctions inferred by STAR? It seems improbable that not a single read was filtered. (Before this, I aligned the raw reads with STAR 2-pass and ran the Picard steps CleanSam, AddOrReplaceReadGroups and Mark Duplicates).
Thanks so much!