Anand Mayakonda

Hi, I compiled it almost ten years ago from a few public resources. I was still new to coding and didn't do a good job documenting. Sorry, I can't say...

Hi, Thank you for the issue. It was indeed a bug - all the input MAFs were being normalized with the first `capture_size`. I have fixed it. Please let me...

Hi, Are you sure the values in `Variant_Classification` column match those provided in `nonSyn`? If you'd like to consider all types as nonSyn, please try as below ```r > laml.maf...

Hi, I'm sorry for not getting back to you sooner. Chromosome names in your MAF appear to have the `chr` prefix already. You do not need to use the `prefix`...

Hi, Sorry for not getting back earlier. I have fixed it. Please try again and let me know if this helps.

Hi Olsen, Thank you for the issue and, sorry for the tardy response. The issue seems to be due to the variant position being larger than the chromosomal length. Could...

Thank you @ShixiangWang for the response. I think there is a mismatch here. `chr2` length from BSgenome.hg38 is smaller than the variant of interest here. ``` > seqlengths(BSgenome.Hsapiens.UCSC.hg38)["chr2"] chr2 242193529...

Hi, Sorry for not getting back sooner. Do your BAM files have the chr prefix?

Hi, Sorry for the delay. - maftools classifies single-nucleotide variants into [Transitions and Transversions](https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html#:~:text=Transitions%20are%20interchanges%20of%20two,ring%20%26%20two%2Dring%20structures.) It's not the same as how bcftools reports for individual conversions. - Please note the section...

Hi @xinghui-guo , We are working on it. It should be available soon.