graphtyper

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Realignment stats

1

Hi Hannes, Would it be possible to include a feature for obtaining some mapping statistics after read realignment to the pangenome? Use case: Comparing the coverage between two regions after...

twesigomwedavid

Including advanced options for graphtyper genotype_sv

4

@hannespetur I was of a view that some advanced options would be great for `graphtyper genotype_sv` ...is there a way to include functionality for this?

twesigomwedavid

support for haploid/different ploidy

1

Hi, I am really interested in using graphtyper for my bacterial genome SNP calling as there is a lot of diversity in some lineages and typical SNP calling pipelines run...

alexweisberg

Related to https://github.com/DecodeGenetics/graphtyper/issues/110 Updates: * paw to [latest `dev` + ARM64 fixes](https://github.com/hannespetur/paw/pull/16) * parallel-hashmap to 1.35 Added a CI job for Linux ARM64. Results could be seen at my [fork](https://github.com/martin-g/graphtyper/actions/runs/3097821664/jobs/5014953708)

martin-g

INFO/AAScore using graphtyper 2.7.4 is missing

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When running Graphtyper 2.7, the info field output included the AAScore field along with the other QC fields. However, when we ran the newer 2.74, the AAScore was not found...

jjfarrell

Hi. I'm genotyping SVs in the HG002 sample. The command I used is ``` for i in {1..22} do $graphtyper genotype_sv $ref_file_folder/GCA_chr${i}.fa $vcf_folder/chr${i}_sv/chr${i}.vcf.gz --sam=$bam_file_folder/chr${i}_surject_chr_sort.bam --region=chr${i} --output="graphtyper_chr${i}" & done wait ```...

tanger-code

Hi, I'd like to ask if Graptyper can reliably call X-chromosome variants on GRCh38-aligned BAMs, and if there's any parameters I should use or something else to note? I.e. with...

Sirtx

Dear hannespetur, hello, I made some mistakes when running graphtyper. My running command is as follows, but the column REF in my VCF file is all N. “graphtyper genotype_sv genomic.fasta...

pingxinxing

genotype wrong

4

```shell ./graphtyper genotype ~/data1/References/human/bowen/Homo_sapiens_assembly38.fasta --sam=NA12878/alignment/NA12878.alt_bwamem_GRCh38DH.20150718.CEU.low_coverage.bam --region=chr21 --threads=40 --prior_vcf=~/data1/References/human/dbsnp/dbsnp138/Homo_sapiens_assembly38.dbsnp138.vcf.gz ``` I encountered an error, and I don't know how to solve it, `constructor.cpp:1248 Found an SV in a non-SV graph at...

lihaicheng7003

Genotype outputs all sites

4

Can graphtyper output the genotyping of all sites in a region, such as mitochondrial 16569bp? ```shell ./graphtyper genotype ~/data1/References/human/Homo_sapiens_assembly38.fasta --sam=~/data1/project10/subdata/1.markdup.bam --region=chrM --output=~/data1/project19/results_chrM --vcf=output_chrM.vcf.modif.gz --force_no_filter_zero_qual ``` I tried this command but...

lihaicheng7003