vcf file alternate allele

Question

[evafinegan]

Hi,

I have a vcf file with multiple samples.

REF ALT
TTTTAA  TTTTAT,TTTATAA,TTAAAAAA

Here is one variant line from the vcf file. There are multiple alternate alleles for the variant position. I want to split the alternate alleles with a tab into different columns each. Then I want to find and compare the lengths of REF variant and largest ALT variant such as:

REF ALT
TTTTAA  TTTTAT TTTATAA TTAAAAAA
6 8

Thank you for any help!

[Ram]

Please look into bcftools query -f to format VCF information in custom formats. You will need to use some python/R/awk to get to the length-of-longest-ALT part.