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The WDL 1.0 spec is now out and supported by Cromwell. The [WDL workflows](https://github.com/broadinstitute/viral-ngs/tree/ct-vphaser-wdl/pipes/WDL/workflows) of viral-ngs should be updated to adhere…
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``` bash
bash-4.1$ java -cp target/kgem-0.7.1.jar:target/dependency/* edu.gsu.cs.kgem.exec.Main 780.sam 1 && head haplotypes.fa
[main] INFO kGEM - [04:49:55 PM] -----------------------------------…
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I am running into an error with the snakemake pipeline installed with easy script. right now I am running just one sample converted from fastq to uBAM using picard tools. I have attached the snakemake…
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The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembl…
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With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has no alterna…
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**Generate second coverage report with different options:**
Currently `bedtools genomecov` is used to create coverage reports for aligned bam files. This is great, but it would be helpful to also hav…
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@marekkokot Is there a test suite you use to verify correctness of kmc and kmc_tools? If there is, could it be checked into github?
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Similar to how we write a spikein report, we should consider adding a report on insert sizes via Picard's `CollectInsertSizeMetrics`.
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## Problem description
readjoiner fails with an assertion:
$ gt readjoiner overlap -readset samp -l 90
# gt readjoiner overlap (version 1.2)
# number of reads in filtered readset = 7960
Assert…
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Hi,
Reported this error when using deplete_blastn_paired.
> BLAST Database error: No alias or index file found for nucleotide database [xxxx.fasta] in search path
Does anyone know why?
T…