trouble in SNP calling using ANGSD

Question

[Jay Chou]

Hello there,I called snp using the newest software angsd, and unlike the traditional software like samtools and GATK which can output the vcf format, this software seems not having valid output format to facilitate subsequent plink analysis. Is there any similar experience in this respect, please give me some advice, thanks!

Answer 1

[andersdetermig]

try the

-doPlink 2

option to generate plink input files (tped/tfam)

http://popgen.dk/angsd/index.php/Plink