graphtyper

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better explanation of graphtyper output VCF

2

Hello, Can you please provide some more details on the format of graphtyper output VCF? I'm interested essentially in 2 points: 1. Variants definitions. Take the following example: Given my...

edg1983

[Question] Is ARM64 a supported architecture?

4

Hello, I’d like to ask whether graphtyper is supported on Linux/Mac ARM64 systems ? Any concerns ? Any positive/negative experience ? Thank you!

markjens

I get the vcf files with graphtyper, but the column of REF and ALT doesn't contain sequence information. For example:  but I want to gain such format, the REF...

zhoudreames

I want to call and genotype SV with population-level by using manta-svimmer-graphtype workflow, but I don't know how to gain the tutorial of the whole process, Can you provide me...

zhoudreames

I do not know how to add an insertion at position

2

 Hello, what is the problem with this, thank you for your answer

zongzone

The genome size is too large to genotype for some genomic region properly !!!

1

**Hi Hannes,** **I encountered a BUG when using GraphTyper2 to genotype SV in the wheat genome. The wheat genome is about 15Gb. If the genome size is too large (more...

yinmou21

COVERAGE model missing for DEL causing AGGREGATED model to fail

2

Hello Dr. Eggertsson, First of all thank you for this very useful software. As I was looking for a way to have each structural variant mentioned only once in my...

Lee-06

What does that mean？（FT=FAIL1/FAIL2/FAIL3！）

1

Hi， Thank you so much for developing such a nice program. The output of GraphTyper2 contains something: FT=FAIL1 or FAIL2 or FAIL3！  What does that mean, please? Thank you...

yinmou21

Segmentation fault Reads with name=xxx both have IS_FIRST_IN_PAIR=1

2

Graphtyper is generating the error below which indicates there is some issue with a read pair in a cram. After the error message, a segmentation fault is generated. This is...

jjfarrell

<DEL:SVSIZE=0+:AGGREGATED>

2

Hi In my result, some DEL length is 0 bp, why is that? Can the SVs of length 0 bp be filtered out? 

anxuan-web