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@ckandoth might need your input on this one:
2016-04-01 00:36:53,319 - merge - INFO - Processing conversion of merges/BLCA/104c8e20-1b29-4d77-9633-359a35be48fb_01_10/tmp/merged.annotated.vcf -> merge…
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I've run all the preliminary steps without problem (HapCut2, prep) but the final 'call' step has been running for over a week now, using 1 cpu, and stable at a couple GB of RAM. It also output (not su…
jfass updated
4 years ago
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In the context of somatic mutations there is no easy way to represent a genotype in the same way as in germline variants. For this reason, some somatic mutation callers, do not provide genotype inform…
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Chris and Sangtae;
This is a follow-up to a bcbio discussion (https://github.com/chapmanb/bcbio-nextgen/issues/2112#issuecomment-338307641) which I thought could use it's own thread. In bcbio we're c…
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Hi!
Is it possible to filter the cancer variants by 'Qual' to, for example, obtain only 'PASS' variants or filter out cancer-germline variants? Alternatively, can the 'Qual' field be sorted so that '…
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Hi.
I tired to run MoCaSeq test pipeline several times but every time FILE ERROR happend.
---- Matched BAM-files? ----
Thu Dec 23 12:34:20 UTC 2021 timestamp: 1640262860
+------------+
| FILE…
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Hello Brad,
I have a question/request about the output from running ensemble variant caller, specifially the format field. At the moment the ensemble vcf file reports the format field from the first …
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Hey Brent,
Long time gemini user, and setting up slivar for my group. We focus largely on singletons and used gemini filters like num_het, num_hom_alt to capture variants that are present in multip…
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Hello, I'm attempting to try out your tool and to start i have tried out:
```
singularity exec -e mergesvvcf_0.0.1.sif mergesvvcf -l delly,manta -o test.out -sv sample.delly.vcf.gz sample.manta.vcf.…
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There seems to be confusion surrounding the use of the GT and AD keys in the INFO field.
The GATK Mutect2 tool would produce a VCF file containing the following GT:AD values for a sample containing…