Hardip Patel

Dear, I have used bwa-mem (0.7.17) for mapping whole genome sequence data from humans. I have hard-masked (all bases converted to N) the Y-chromosome sequences for female samples lacking the...

Assertion failed in readjoiner assembly step

6

Hi, While running the gt readjoiner assembly, I received the following error. ``` Assertion failed: (nofreads == nofreads_i), function gt_readjoiner_assembly_build_contained_reads_list, file src/tools/gt_readjoiner_assembly.c, line 472.` ``` gt version info: ``` gt...

Hi, I was trying to compile v0.2 (release) using intel compiler instead of gcc for our systems. I got following warning. ``` icpc: command line warning #10006: ignoring unknown option...

rework Record inputs, dependent and mutually exclusive parameters

2

Dear I noticed he following discrepancy in the User Guide for the [item no. 2.10](http://www.commonwl.org/v1.0/UserGuide.html#Record_inputs,_dependent_and_mutually_exclusive_parameters). I am not the expert so didn't know what the correct answer is and therefore...

PBSPro Backend Configuration

2

Hi We are trying to setup the cromwell + wdl for genomic analyses at the [National Computational Infrastructure HPC facility](https://nci.org.au/systems-services/peak-system/raijin/) in Australia. This HPC runs bespoke configured PBSPro. I have...

**What do you want to know?** Can we please add the feature to include repeat class and family information in the GFF output. This helps with downstream processes such as...