search

grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
29 stars 2 forks source link

cannot determine the root allele #12

Open coopergrace opened 4 years ago

coopergrace commented 4 years ago

I've come across an issue when trying to convert .acf to .beta for use with BetaScan.

I can generate acf files using the command: glactools vcfm2acf --onlyGT --fai ref.fai pops.chr9.vcf > pops.chr9.acf

and the format looks fine, e.g.

#chr    coord   REF,ALT   root       anc     pop1    pop2    pop3    pop4
9       5895    G,T       0,0:0      0,0:0   49,60:0 0,0:0   0,0:0   0,0:0
9       5929    A,G       0,0:0      0,0:0   0,0:0   14,16:0 0,0:0   0,0:0
9       5979    T,G       1,26:0    1,26:0   0,0:0   0,0:0   0,0:0   77,5:0

where each population was extracted from a multi sample vcf with the vcftools flag --mac 1. I then merged the samples into the populations and set the root and anc as detailed in the README.

Converting from acf to beta: glactools acf2betascan --useroot pops.rooted.chr9.acf.gz | gzip > pops.rooted.chr9.beta.txt.gz

is when I receive the error for the majority of positions: Cannot determine the root allele for 9 5979 T,G 1,26:0 1,26:0 0,0:0 0,0:0 0,0:0 77,5:0

But then it reports: Program ACF2BETASCAN looked at 1227 records, terminated gracefully

Yet the resulting beta.txt files are empty. Any ideas please?

Cheers

Cooper