Question

Vcf File Consensus Sequence

1

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12.7 years ago

Kwame ▴ 10

Hello,

Are there samtools command to get a consensus sequence from a vcf file?

vcf • 3.7k views

ADD COMMENT • link updated 12.7 years ago by Swbarnes2 ★ 1.6k • written 12.7 years ago by Kwame ▴ 10

score 1 · Answer 1 · 2011-09-14

1

Entering edit mode

12.7 years ago

Swbarnes2 ★ 1.6k

There is a perl script called vcfutils in the bcftools folder that will make a consensus from an all-loci vcf file. It will ignore indels, only making a lower-case letter windows around them.

ADD COMMENT • link 12.7 years ago by Swbarnes2 ★ 1.6k