Convert mpileup file into dataframe
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!
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1 answer
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
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