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Hello,
I really like the pipeline but I have a suggestion for a change to incorporate into a new release. I'm working on metagenomic studies where I have made a reference with a ton of viral sequen…
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Todo:
- [x] convert BAMs of legacy samples to CRAM for diagnostics (WGS and WES) when GRCh38 with false duplications masked was used
- [x] correct for GRCh38 with false duplications not masked
- [x] r…
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### Operating System
Other Linux (please specify below)
### Other Linux
RedHat 8.9
### Workflow Version
v2.4.1
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No r…
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When I run the "checkm coverage" i keep getting the "NameError: name 'pysam' is not defined".
I am using sorted and indexed bam files generated through Bowtie2+samtools.
I am using CheckM v1.2.3 wit…
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Hey,
I tried the script on my data set (which is a fragmented bacterial genome extracted from a metagenome).
```bash
Rscript --vanilla plot_BAM_density.R -f ../GCA_012799365.1_ASM1279936v1_ge…
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Hi @GermanDemidov,
Thanks for the precious tool and the great documentation on it.
I am considering to use the tool for germline (and eventually mosaic) CNV calling in panels and WES scenarios.
…
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Good evening,
`ngsPool` provides `poolSFS.R`, a script which estimates a one dimensional SFS from the `SAF.GZ` output file. Is it possible for other software to read pairs of "sample allele frequen…
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Hi,
thanks for developing such an efficient and needed tool!
I have been looking around this and other repositories of ML4GLand to find examples of best practices to read a genome fasta and a ba…
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## The need
I was profiling a bam file when I noticed that a massive amount of my reads were not used:
```
WARNING
====================================================
There were 553 reads pres…
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Hi Kris (and Karthik),
My student is trying to bin contigs identified by VirSorter using vRhyme. He is using as input contigs identified by VirSorter as viral, as well as sorted bam files that were…