biozzq
biozzq
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....
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...
Dear all, When comparing graph genome and linear genome in short reads mapping, I found that graph genome did not improve the short reads mapping. Has this phenomenon also occurred...
Dear all, When learning how to detect SVs based on the `pggb` constructed graph genome using `vg giraffe`, I found that the results are a bit strange. And this may...
Dear all, Can I use minigraph+Giraffe to achieve genotyping of structural variants in the framework of the graph genome? Thank you in advance. Sincerely, Zheng zhuqing
Dear @brentp When calling population CNVs, I would use different tools (e.g., Lumpy. Delly, and Manta) to call SVs for each sample, and thus I will get three VCF files...
Dear @brentp The BAM file was generated by BWA-MEM (alignment without -M) and picard (remove duplication). When using it to detect CNV using smoove using following command, the program failed...
Dear @pd3 I am using bcftools roh (version 1.12; `bcftools roh -G30 -e - -O r vcf.gz`) to detect regions of autozygosity in whole genome sequencing data. The vcf.gz contains...
Dear all, To prepare the gtf file used in `rnaseqc`, I first converted the gff file to gtf file using following command, `gffread-0.12.7.Linux_x86_64/gffread -T -o out.gtf input.gff`, however it give...
Dear all, I am learning how to better use gemBS to analysis the whole-genome bisulfite sequencing data. During testing using the example data, I found that it is difficult for...