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.
SortSam is failing due to Error Parsing SAM file: ("Tag of type i should have signed decimal value")
I am attempting doing variant-calling on a genomic sample, however it failed at the SortSam step due to the following:
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Tag of type i should have signed decimal value; File HBCC-DNA-CER-13309.sam; Line 124767604 Line: E00218:353:HC32YALXX:5:2212:7395:55227 83 chr20 27310902 0 151M = 27310664 -389 GAGCGCTTTCAGGACGACGGTGAAAATGGAAATATCTTCCAAGAAAATCTGGATAGAAGCAATGTCAGAAACTTTTCTGTGATGGATCTACTCAGCTAACAGAGTTGAACCTTTCTTTTGAGAGAGCAGTTTTGCAACACTCTTTTTGTGG ?=<7>@@@[email protected]>>>9>>9>>>>???>>>6??>?=>??>>>??>???>>>>===>>=>>==>=====>=>>=>>>>=>==========>>=>==>=>>>==>=>=>=<>===>>=>=>=<==<=<==<==>=>===>===>=>>>>??=><> NM:i:1 MD:Z:50A100 AS:i
The SAM file was generated using BWA MEM.
I am unfamiliar with this issue. How do I resolve it?
Post edited by claudiadast on