Annotating VCF with centimorgan information (cM)
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15 months ago
4galaxy77 ★ 1.7k

I often need to know the interpolated cumulative genetic distance in cM across the genome. I am aware of some software, such as shapeit4, which outputs an INFO field in the vcf:

##INFO=<ID=CM,Number=A,Type=Float,Description="Interpolated cM position">

9   204201  rs10964134  G   A   .   .   AC=0;AF=0.170557;CM=0;AN=2  GT  0|0
9   204485  rs613181    T   C   .   .   AC=1;AF=0.227743;CM=0.000228;AN=2   GT  0|1
9   206132  rs10757083  A   C   .   .   AC=0;AF=0.218573;CM=0.002086;AN=2   GT  0|0
9   212486  rs118002206 G   A   .   .   AC=0;AF=0.0163388;CM=0.00778367;AN=2    GT  0|0

It's possible to manually calculate and then use bcftools annotate to add it in, but this is a bit of a hassle.

Does anyone know of any software which I can give a) my vcf, and b) a genetic map, which will then annotate the vcf with an INFO field which gives the interpolated cumulative genetic distance?

snp vcf • 574 views
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