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Hi,
VarDict is mislabeling a SNV as being AMPBIAS for 2 of my three samples. As you can see in the picture, there are multiple overlapping amplicons that contain the SNV.
![igv_snapshot](https:/…
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Hi!
I am currently trying to run the following command:
`racon -u -f -w 50 -q 9 ../trim50_dem_q9/barcode02.fastq ../minimap2_output_x_map_ont/aln_2.sam ../gene_references/msp2_pf3d7_02026800.fasta`
…
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Hi!
I am currently trying to run this software to see the number of haplotypes I get across 20 samples that have been demultiplexed in the past. For this, I am running setupTarAmpAnalysis after I cre…
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Hi everyone,
I'm a beginner using spades 3.11.0 since March2019 , trying to practice doing some assemblies via getting SRA files from papers that i'm interested in.
What I have done:
1. Pulled …
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Hi,
In the VCF file resulting from my paired sample analysis I see these types of variants
TYPE=Complex
TYPE=DEL
TYPE=Deletion
TYPE=DUP
TYPE=Insertion
TYPE=INV
TYPE=SNV
I don't understand…
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This is a minor issue. Maybe the two warnings are worth correcting.
```sh
# where swarm is swarm's repository
cppcheck --enable=all swarm/ 1> /dev/null
```
returns two warnings, and several varia…
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here is my code, thanks a lot
/data/ngs/softs/VarDict-master/vardict -G /data/ngs/database/GATK_Resource_Bundle/hg19/ucsc.hg19.fasta -f 0.01 -N NGS201911-1SZ -b "NGS201911-1SZ.tumor.sorted.dedup.re…
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Using NerConverter in some situations produces an exception:
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
## Description
In a pipeline wirh nerconverter and with s…
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I'm really liking the gVCF support. For some sparse sequencing assays (panels of amplicons for instance) the `--gvcf-chunk` parameter is critical for limiting memory usage. I'm assuming this has som…