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Is there a way to apply different (left|right)_trim values to R1 and R2?
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I am using delly0.8.1 to call SV. My sample is a pair of normal tumor tissues with a depth of about 1000x. This is my script:
$delly call -g $ref -x $excl -o $dellyout/${tumor}_${normal}.bcf $tdata/$…
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- [x] Can we change mixed_cfdna_msk_2019 to cfdna_msk_2019? (it would be great if we can aviod using `mixed` in study ID going forward as mentioned in #256
- [ ] It would be great to get the time …
jjgao updated
4 years ago
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Hi,
I am running some different samples (RNA vs cfDNA) through `somalier` and one of them came out with a very low relatedness, even though 77 (out of 78) sites are IBS2:
```
#sample_a sample…
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**Snakemake version**
5.15.0
**Describe the bug**
Specifying resources for qsub in the rule config works for "shell:" syntax.
When using a wrapper script, it gives "unexpected keyword" error…
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Hello!
I was wondering if anyone has encountered this problem when loading the study "cesc_tcga_pan_can_atlas_2018".
Is there a known work around?
cesc_pan_2018
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The final report rule in BS seq uses `run` instead of `shell`, which means we cannot see what's happening inside snakemake with the option `printshellcmds`.
This enormously increases the difficult…
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hello Dr.Niu,
I had test MSIsensor2 for cfDNA sample.
There is some issues confused me.
At First I try the Tumor-Only for the cfDNA sample:
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There is the ability to get purity, ploidy, and major and minor copy numbers with this software, which sets it up perfectly to use output for subclonal clustering. However, I have not been able to ea…
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I tried running the "Cluster" function, but got this. What is wrong here?
Clustering and calling consensus on 24 chunks (Thread Region RamUsed Time):
ERROR: could not extract a BMF barcode from th…