Amay Agrawal

How to choose right blastp minimum precent indentity and mcl inflation value?

1

This is more of a query instead of an issue. I am a bit confused about how to choose an optimum value of minimum percentage identity for blastp as well...

Suggestions needed for the whole-genome model output

1

Hi, This is not an issue but more of a question from my side. I used the LMM model implemented in Pyseer to perform my GWAS analysis and figured out...

Issue while choosing the reference path for genotyping

4

Hi, I am facing an issue regarding the reference path that pandora uses for genotyping the variants. It is basically using the less frequent supported path instead of most frequent...

Runtime for pandora compare

6

Hi, I am using `pandora compare` to call out the variants after building the pan-genome reference graphs and indexing them using `pandora index`. Although I am using multiple threads, it...

Understanding Genotype output in the VCF file generated using Pandora map and compare

6

I am using `pandora map` to align the reads against the pangenome reference and call out the variants using the `--genotype` option. I ran the pandora map command using the...