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I am getting a Null Pointer error while running Kourami on a custom built IMGT HLA alignments version 3.37.0 and using 1000 genomes NA12878 GRCh38 aligned bam file. I went through the steps explained …
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Сделать выбор между _Bowtie 2_ и классическим _BWA-MEM_ было непросто, и я предпочёл первый из перечисленных буквально на основании степени дружественности документации. _BWA-MEM2_ существенно превосх…
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Hello,
I have a rather difficult problem. I am aligning several wgs samples, each about 100gb filesize, and for one of them bwa-mem2 avx just stops at 17gb without any error. bwa-mem2 sse4.1 stops at…
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## BWA Short Reads
Bowtie2 is fast and has similar results to BWA but is generally regarded to have higher accuracy.
#### BWA modes
[From this guide](https://hbctraining.github.io/In-depth-NGS-Da…
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Hi
I've recently come across a forum (https://www.biostars.org/p/89088/) which mentions that bwa mem should be run with Phred+33 Illumina reads instead of Phred+64. My Illumina library is Phred+64, a…
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Dear developers:
Hello and recently I was using VG to make a variant graph of a plant species and I want to compare the number of reads of one accession mapped onto the graph-based genome via vg gi…
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Support the following mappers
- [ ] BWA-MEM
- [x] Bowtie 2
- [ ] NextGenMap
- [ ] BBMap
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Hi @ksahlin !
sorry for bothering you again!
I am trying to run GATK haplotypecaller on reads mapped with Strobealign. The Haplotypecaller ends with an error:
`java.lang.IllegalArgumentException:…
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Hi,
I'm currently evaluating VarDict on a synthetic tumour dataset similar to the ICGC DREAM set. I'm using VarDict version 1.5.2 with the following commands:
Call variants:
```shell
$ VarDi…
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**Is your feature request related to a problem? Please describe.**
I have a rule using the [bwa mem wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/bwa/mem.html) that sometimes …