HanC

Annotate fail to add INFO when match structural variation by POS,~ID,REF,ALT

3

Hi, I am using bcftools 1.15.1. I want to add INFO for a vcf file of structural variations. The vcf is like: ``` chr1 10627 ID1 N . PASS some_INFO...

Inconsistent force calling with original discovery calling

6

Hi, I am using latest cute SV (v2.0.0) and want to apply cuteSV to PacBio CLR data for population-scale analysis. I first run cuteSV on each sample and then do...

## Bug Report ### Affected tool(s) or class(es) MarkDuplicatesSpark ### Affected version(s) - Latest public release version [4.4.0.0] ### Description I am working on 40X human WGS data, running MarkDuplicatesSpark...

Best practice for estimating contamination within the same ancestry

1

Hi, I am wondering what is the best way to estimate contamination for samples with the same ancestry background. In my work, all samples are East Asian. If I want...

Questions on data bundle and SV genotyping

1

Hi @jonassibbesen , Thanks for providing this great tool. I am now trying to download the data bundle from the link you provide. However, it always failed after ~1GB data...

Interchromosomal misjoin

2

Hi, I am using hifiasm 0.19.8-r603 to do human genome assembly using hifi-only data. After the assembly, I found there is a interchromosomam misjoin reported by `paftools.js misjoin -c centromeres.bed...

vg convert unable to write rGFA tags

3

**1. What were you trying to do?** I would like to convert haplotype sampled GBZ graph to GFA, with GRCh38 path written as rGFA tags. **2. What did you want...

**Describe the bug** In the output of `vcfwave`, the phased genotypes are not consistent with the input VCF. **To Reproduce** Here are some examples of the incorrect phased genotypes. Input...