.fai file mentioned in page: http://www.popgen.dk/angsd/index.php/Input corresponds to reference fasta file. Index your reference fasta file and this would create a fai file. This fai file should be supplied to the command. Example command would be (assuming that your reference sequence used in alignment is reference.fa and vcf file is sample.vcf):
#for using GL tags
./angsd -vcf-gl sample.vcf -fai reference.fa.fai -nind <sample numbers in your VCF> -domaf 1 -out <output_file_name>
#for using GP tags
./angsd -vcf-gp sample.vcf -fai reference.fa.fai -nind <sample numbers in your VCF> -domaf 1 -out <output_file_name>
One cannot create a fai from VCF file. VCF indexing produces idx files and fasta indexing generates fai files, in general.
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3.4 years ago by
cpad0112 ♦ 11k