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Hi,
Thanks for developing this very useful and much needed tool!
I am running step4 option A and it seems like it cannot identify any valid SAMrecords in my file.
The command I am running is …
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```
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C
/srv/gsfs0/projects/cho/riboseq/bam/R10_Rluc_control_arsenite_R1.hg19.bam -O
R10.genebody
.
What is the exp…
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Hello!
I've seen in the changelog that for DUPs the start position was changed from 0-based to 1-based. What's the case for the rest of the variants, are they 0-based or 1-based?
Best regards,
…
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for uploaded BAM files
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Hi all.
As has been discussed previously we in Umeå has started to work on an extension that will enable 3rd party variant interpretation tools integration in scout. But we have also received fund…
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```
What steps will reproduce the problem?
1. 我的路由器是tp-link
841n，没有jffs空间，要如何才能使用这个路由翻墙方案？
2.
3.
What is the expected output? What do you see instead?
What version of the product are you using? On…
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EDIT: I understand the problem now. I have some selfing in the population which will cause some level of homozygosity for the alternate allele and hence this will not work.
[Keeping this issue on fo…
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After merging #80, a results table with adjusted p-values and log fold change across replicates can be generated.
This is a reminder that a plotting function for such bins using a pval or/and logfc…
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## Bug Report
### Affected tool(s) or class(es)
- `HaplotypeCaller` with the arguments `--max-mnp-distance 5`.
### Affected version(s)
- gatk version 4.0.12.0
### Description
For a g…
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I've run into an issue with the likely misclassification of the strandedness of certain splice junctions. I'm working with a strand-specific RNA-Seq library for A. thaliana and generated a BAM supplem…