graphtyper

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Thank you for your brilliant work on Graphtyper2. I have encountered one issue during the use of Graphtyper2. For example: SV=chr1:54719:UG, END=54720, End-Start=1, but SV size =50 SV=chr1:3212695:DG, END=3212826, End-Start=131,...

whtop

How to best filter duplicate calls in the output VCF to get one call per variant?

6

Apologies if I missed this information. I noticed that the same variant can have multiple entries in the output VCF. The ALT field seems to suggest it's because they represent...

jmonlong

Genotyping SVs from other callers

3

Dear Hannes Thank you so much for developing such a nice program. I used GraphTyper on Manta and CNVnator outputs (after getting the union of SVs by svimmer) successfully. However,...

dr-ashu-geno

Not all variants with aggregated tag and many variants with low quality genotype

1

Hi @hannespetur The genotyping accuracy of structural variants has a large impact on the subsequent analysis. Currently, I usually use `graphtyper (the latest version)` and `paragraph` to realize this progress....

biozzq

Dear @hannespetur I found many variants are with "PASS" for `FT` but not `FILTER`, as the following example. Should I filter out these？Thanks for your attention. ``` 1 273082885 1:273082885:FG...

biozzq

Hi! I am using `graphtyper genotype` with the `--vcf` flag to genotype a specific set of input variants. However, it seems that Graphtyper does not only genotype these variants, but...

ivargr

Can graphtyper be used to genotype cancer samples ?

1

Hi, i have a query wrt to the tool and its utility in genotyping cancer samples ? what model does it assume in genotyping, is it diploid model ? Can...

rbr7

No OLD_VARIANT_ID?

1

Hello, thank you for making this awesome tool! I have a question about the "OLD_VARIANT_ID" field. I regenotyped a VCF of SV sites called with Manta. In the Graphtyper output,...

kmegq

Long-read assemblies

6

I'd like to include the Long-read assemblies file when identifying structural variations.How do I get Long-read assemblies SVS_VCF files?

z1242099843

Error in genotype reading temporary input fasta

4

I've started a run of graphtyper with a command for each chromosome of my reference: graphtyper genotype --threads 16 --verbose --sams=bamlist --region=H1_8_48-4_1 REF.fna graphtyper genotype --threads 16 --verbose --sams=bamlist --region=H1_8_48-4_2...

alexweisberg