vcf file alternate allele
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!
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evafinegan •
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evafinegan •
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Please look into
bcftools query -fto format VCF information in custom formats. You will need to use some python/R/awk to get to the length-of-longest-ALT part.