Select one variant from multiple in ALT in VCF file

Question

[FL512]

Let's say if my VCF file has a C in REF and A,TTA in ALT (sometimes even more than three variants in REF column though), which would interrupt my analyses because the tools I would like to use required only one variant in ALT.

Therefore, I want to select one ALT based on the value of minor allele frequency (I believe this criterion is reasonable). Header of my VCF and each data are as follows;

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr1 10000 . C A,TTA . . DP=100;ECNT=2;MBQ= .......... GT:AD:AF:DP 0/0:22,10,0:0.290,0.031:30  0/1/2:60,18,6:0.210,0.073:90

How could I make a final VCF like

chr1 10000 . C A . . DP=100;ECNT=2;MBQ= ..........

which I want keep the variant that has a highest minor allele frequency.

Are there any tools or any kind of script available, or if someone has already addressed this, please kindly let me know! Thank you.

Answer 1

[Medhat]

bcftools norm -m is able to split multi-allelic sites, then you may filter by allele frequency

[FL512]

Hi Medhat,

Thank you very much for your quick response. I took a look at the bcftools instruction and looks like that is what I was looking for. I will give it a try anyway.

Thank you again!