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Current version looks like:
```
flowr run x=bam_mutect tumor_bam=tumor.bam normal_bam=normal.bam tumor_name=TCGA-00-ABCD-01 normal_name=TCGA-00-ABCD-10 out_prefix=tumor_normal platform=local execute=…
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Would it be possible to add a feature to run meryl-lookup exclude/include on a BAM instead of a fasta and output BAM? This would be very useful for filtering reads from PacBio or ONT data in their or…
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Will it be possible to have a read tag for the MAS adapter used in the segmented bam file so that we can split the bam file if needed? Like if we are using 10 MAS adapter for ligation; can we split th…
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I think there is **possibly** an inconsistency in the location of the application of the Batch Normalization between the paper and the code.
## 1st instance of possible inconsistency:
[The paper ]…
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Hi Alex,
Thanks for the great tool!
I'd like to plot sequencing saturation like cellranger. I wonder if I can get the accumulating saturation from the bam file.
according to this: https://github…
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Thanks for the fantastic animal models! While compatibility with Quark's variant animal textures is implied on BAM's CurseForge page the feature doesn't seem to be working in 1.19.2. Even if you disab…
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Howdy,
I am running the following command to genotype a short read to a reference and I get the "invalid BGZF file: does not end in proper EOF marker" error. I haven't edited any of the files since…
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* Make SAM and BAM records display similarly
A SAM and BAM record contain basically the same information. So they should be displayed similarly in the REPL.
* Create SAM-to-BAM conversion function…
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# Inconsistent BAM flag accessor functions
Currently, it's possible to create a spec-compliant BAM record with the following behaviour:
```
julia> BAM.hasrefname(record)
true
julia> BAM.refna…
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I am seeing a segmentation fault:
```
$wham_dir/bin/WHAM-BAM -m 2 -q 15 -p 10 -x 4 -t $tbam -f $reflib \
1> ${oprefix}_wham.vcf 2> ${oprefix}_wham.out
Aborted (core dumped)
less ${vcf}.out
INFO: …