straglr

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Not all loci in output bedfile

2

Dear @readmanchiu, I am using straglr via the vip pipeline (https://github.com/molgenis/vip/), as described in an earlier thread. Here, we use as an input a bed file with loci. However, I...

ljohansson

Could Gender support and VCF output be added?

4

Dear @readmanchiu, We are using Straglr in our pipeline (https://github.com/molgenis/vip/) to call STR's on nanopore data. Since all the modules in our pipeline are build to have VCF input and...

bartcharbon

refactor: use dataclass for structured tsv reads

4

### Changes - Create a TSV structure to hold start, size and strand. - Bind the current read to a variable instead of repeatedly indexing into support. - Create a...

lavafroth

Interpretation on <output_prefix>.tsv

1

Hi there, I've received an output file, and according to the readme, the allele column should indicate the allele to which the support read is assigned, based on the genotype...

HLHsieh

Calling complex STR patterns

1

Dear @readmanchiu, Some of the STR's we are interested in have a more complex pattern instead of a simple repeating sequence. e.g. something like (TTTTA){5}TTA(TTCTA){5} (5 TTTTA's followed by a...

bartcharbon

Genotyping amplicons?

1

Hi, Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I...

adbeggs

Repeat Interruptions

11

Hi, I was wondering if stragler is able to deal with repeat interruption. For some diseases we can see interruptions of the repeats. Like for Huntington, where the normal repeat...

stefandiederich

Problem with --trf_args

1

No matter what values I assign to --trf_args, I get this error: `straglr.py: error: argument --trf_args: expected 7 arguments` For reference, here is the command I am running ``` sbj=PBMC_XXXX...

ilariastewart