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Q1. I am looking for a way to remove SAM alignments that have too much soft or hard clipping.
eg. a 150bp read with `30S80M40S`
I can't seem to find a way to do it with tools from the `samtools…
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In GitLab by @hoelzer on May 27, 2021, 09:54
Could be interesting to test `minimap2` as aligner instead of `EMBOSS-stretcher`
E.g. the developer just announced that
> Minimap2 v2.19 released with …
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hi,
When I was running sveditor.py script to add CNV to BAM files, it had an error"Failed to open file ./sv_out/tempDir/edit.remap.bam".I checkd every script in VarBen , i didn't find which step …
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Python code is slow for the amount of alignments we might have, it's better to replace it with something speedier i.e. [parasail](https://github.com/jeffdaily/parasail) ([python bindings](https://gith…
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### Description of the bug
```
nextflow run main.nf \
--input https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/samplesheet_test.csv \
--fasta 'https://github.…
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Hi, thank you for your work. I'm just installed RASflow by the Conda environment with the yaml file env.yaml like the tutorial and tried to run the example changing the project name and even another s…
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I have some Enzymatic methyl sequencing data that I am trying to align using bwa-meth. However, I am encountering the following issue in parsing of the sam file that the aligner is generating when I t…
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### Instructions
gatk version 4.4.0.0
When I run gatk GenotypeGVCFs, it shows this error：
A USER ERROR has occurred: Bad input: Presence of '-RAW_MQ' annotation is detected. This GATK versio…
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### Description of the bug
I’m using v3.9 with `--save_umi_intermeds` and `--save_align_intermeds` to save all BAM files. After pipeline finishes, I find these BAM files in `results`
```
$ find res…
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Hello,
I'm using the following command with braker 2.1.6:
```bash
braker.pl --genome genome.fa --UTR=on --stranded=+,- --bam=merged_fwd.bam,merged_rev.bam --softmasking --cores 48
```
I get t…