Jin Seok (Andy) Lee

"None" value in COVERAGE leads to an error with pyvcf

4

There are cases where Sniffles2 reports some of the "COVERAGE" field as "None" (e.g. "None,None,100,None,None"). As a result, reading a Sniffles2 VCF file using pyvcf throws the following error: ValueError:...

Translocation and Inversion

2

What are the best ways to encode a translocation and an inversion in `.gfa` file format? Could you please provide an example for each variant? Thank you!

mafR.clust is NA for all rows

3

I am running FACETS on Whole Exome Sequencing (WES) data. I get NA for all rows in the mafR.clust column. I see that cval of 100 in the procSample function...

Iterating through vcf.Reader deletes data

1

``` file = "some_file.vcf" vcf_reader = vcf.Reader(open(file, 'r')) for record in vcf_reader: print(record) for record in vcf_reader: print(record) ``` The second for loop doesn't print anything as vcf_reader is empty....

Request for fastq.gz read ID format change

2

In the `fastq.gz` that Dorado outputs, I see that a semicolon is sometimes included as part of the read ID. A semicolon is used to separate attribute-value pairs in the...

Matching read IDs for each transcript

1

I want to see which read IDs support each assembled transcript. Is the following the correct way to do this? 1. The transcript ID is the value corresponding to `s`...