I am trying to prepare my vcf data for working with ANGSD. At first, I converted my vcf file to bed file using plink. Then tried bedToBam of BCftools to convert it to bam format. The problem is, a compressed file is generated which is not accessible. Is it happening due to the difference in the chr name in vcf and genome file as vcf file contains only the chromosome number while genome file contains 'chr'?
My another question is, what will be the genome file when I'm working with vcf files that has population specific snps in bcfToBed? The final question is, for such type of data what will be the ancestral sequence in fasta format for ANGSD?