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**Snakemake version**
5.10.0
**Describe the bug**
For each of [bwa index](https://github.com/snakemake/snakemake-wrappers/blob/master/bio/bwa/index/wrapper.py#L22) and [bwa mem](https://github.…
vsoch updated
4 years ago
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BWA-MEM command not set proper pair flag，perhaps because BWA not infer insert size characteristics. Is there some ways or tools to revise the flag value , for example revise 81 to 83, mate revise 161 …
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I have noticed that insert sizes from BWA-MEM seem to start high at the beginning of a chromosome, and drop down towards the end. This isn't really an issue (feel free to close and ignore) but I wante…
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Hi, I run the HERA using test data and got an error about bwa mem.
I run the code below and got an 1.pbs file,
perl $Working_Script/09-Qsub-Pair_Alignment.pl list_outer_pacbio.txt $Working_Script $q…
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### Description of the bug
As a minimal example, I am locally (on a system with 24 cores and 128 GB RAM) running joint germline with just two WES samples with this nextflow.config file
process {
…
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Hi,
I have mate-pair data and need to find SVs using your tool (SVachra). I can see in your previous answer that you have recommend to use bwa-mem for the alignment but I have highly doubt that bwa i…
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Thanks for your great work in developing Chromap, an ultrafast aligner for chromatin profile alignment!
In the paper, you mentioned that Chromap is much faster than popular aligners such as BWA-me…
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**Snakemake version**
8.10.7
**Describe the bug**
If option --drma_logs is used, snakemake crashes
**Minimal example**
```
$ vi snakemake-tutorial-v8+.yaml
>>>name: snakemake-tutorial-v8+
…
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Bug report by @irosenboom
It was reported for 2x150bp Novaseq reads that bwa mem performed alignments with extensive softclipping.
For example, some alignments were of 18bp with 82 bp simply so…
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# Click through:
1. Suppose you are starting at a BRC-analytics page listing available genomes:
2. No…