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?
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.
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