Convert mpileup file into dataframe

Question

[kirillkirilenko]

I have a simple .mpileup file:

...
2R  30249   A   3   ,.. BkF
2R  30250   C   3   ,.. BkF
2R  30251   G   3   TtT BkF
...

And I want to convert it into dataframe like this:

chr   POS   Ref   Alt
...
2R  30249   A   A   
2R  30250   C   C   
2R  30251   G   T
...

As far I understand I can not perform Variant calling, because I need all records including common with reference. I can write a script, but I think samtools or bcftools allow to make something like this, but I couldn't find it... Thank you in advance!

Answer 1

[ATpoint]

No, don't do any custom data fiddling. Follow the manual of bcftools for variant calling, it covers all you need: https://samtools.github.io/bcftools/howtos/variant-calling.html