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Hi, I know that there is a section which says that BAM file should be used from BWA MEM, but does this mean that we could also use BAM file created by GATK best practice workflow, which means that BAM…
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Hi, thanks for creating this wonderful package!
Is it possible to efficiently extract the entries from a file (BED/BAM/VCF) that correspond to a given set of intervals without having to go through…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
latest
### Workflow Execution
Command line (Local)
### Other workflow execution
_No response_
### EPI2ME …
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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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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/217) by Milad Mortazavi (Bitbucket: [Milad Mortazavi](https://bitbucket.org/Milad Mortazavi), ).**
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```
This functionality should exist. Just haven't had time to add it yet.
```
Original issue reported on code.google.com by `aaronqui...@gmail.com` on 17 Jul 2010 at 12:31
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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: …
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Hi, Leung,
I'm encountering an issue converting SRA files into BAM files with headers for subsequent analysis.
I've been using the following command to convert the raw SRA files into subreads BA…