population mutation spectra?

[goldmich]

Would be awesome to output the mutation spectrum for a group of individuals - effectively colsums of a ksfs, i.e. input data for the Harris & Pritchard 2017 heatmaps. Thanks!

[wsdewitt]

@goldmich Here's a workaround to get this on the command line:

mutyper variants <fasta> <vcf> | mutyper ksfs - | cut -f2- | awk 'NR==1{print $0} {for (i=1;i<=NF;i++) sum[i]+=$i} END{for (i in sum) printf sum[i] "\t"; print }'

Explanation:

• the cut command removes the sample_frequency column from the ksfs output
• the awk command prints the mutation types, then the ksfs row sums for each

[wsdewitt]

closed in 17d82cf