jjfarrell
jjfarrell
This page (https://biocontainers.pro/tools/gatk4) was last updated in Feb, 2022 and does not list the latest GATK versions. It shows the command to install gatk4:4.2.4.0--hdfd78af_0 and not the latest version. But...
Graphtyper is generating the error below which indicates there is some issue with a read pair in a cram. After the error message, a segmentation fault is generated. This is...
Using a large library of breakpoints, a job was submitted on the GIAB HG002 sample for each chromosome using 8 threads. Most chromosomes completed in under 8 hours except chromosome...
Why is the filter a PASS for these 3 variants but the FT=FAIL1. Also what is the best software to compare these calls with the GIAB benchmark? The Ref All...
Will the --forcedGT option work for candidate SVs generated from Manta? If so, is any reformatting be required for the Manta SV call set to make it compatible?
It would be great if manta had a forcedGT option similar to what is in Strelka2 has. Are there any plans to implement that? This option genotypes a list of...
We are getting an error when our sample size goes above 50,000. The PC-AIR step results in just NAs for all the PCS. At 45k samples, it runs fine. Originally...
When running combine, the following error occurs. Any suggestions? ``` [09/03/2020 23:18:18] You are using BayesTyperTools (v1.5) [09/03/2020 23:18:18] Running BayesTyperTools (v1.5) combine on 2 files ... [09/03/2020 23:19:28] Finished...
The prior vcf that is distributed BayesTyper has a very comprehensive list of SVs. Now there is a recently released SV vcf from gnomAD would be great to add to...
In the prior vcf file, there is a lot of details on the origin of the calls. However, it is not retained when combined with another vcf and all these...