-
Hi,
When I was converting the cram to the fastq, I found the code in your WDL workflow:
> seq 0 ~{in_nb_chunks} | head -n ~{in_max_chunks} | parallel -j ~{in_cram_convert_cores} "samtools colla…
-
Hi,
I want to use this software to call STR in my WGS data, when i install it, an error occurs .
The following error is happening in the **make** step:
make[2]: Warning: File 'genotypin…
-
Hi,
I am facing an issue regarding the reference path that pandora uses for genotyping the variants. It is basically using the less frequent supported path instead of most frequent supported path a…
-
Expected Behavior
--------------------------------------------------------------------------
To differentiate samples, sequence barcodes are used in different wells of the genotyping plate. This me…
-
Hi,great author,thank you for method provided for SV typing.I encountered a problem when running the SV_genotyping code,for the BAM file generated after the re-sequencing data of the sample is compare…
-
@davidbenjamin We might be able to share some code with contamination calculation, etc. Tangentially related, we also should unify the pileup-based tools at some point. Low priority, we can discuss …
-
I have a slight concern/misunderstanding regarding error rate.
We have two separate error rates in pandora.
1. `-e,--error_rate` which defaults to 0.11 for nanopore and 0.001 for Illumina.
2. …
-
Hi,
I'd like to report a small bug that I occasionally see happening in my data-set;
- Extremely large deletions are often called as homozygous while clear heterozygosity can be seen in read-mappi…
-
Hello,
I have been trying to genotype structural variants from a graph made with minigraph-cactus, by mapping short reads with vg giraffe, then using vg pack and vg call to get a vcf. This runs wit…
-
Hi again, and thanks again for all the help with the great pipeline!
Now this error:
> ERROR ~ Error executing process > 'HADGE:run_multi:gene_demultiplexing:variant_freebayes:freebayes (sid456)'…