Hi all,
I'm currently working on a project that involves determining the ancestry of an admixed population. I'm having problems with the phasing part of it, and it's because Beagle keeps giving me an error. I'm using data from the 1000 genome project, of which I took a subset using vcftools. When I try to use the vcf files generated by vcftools as input for Beagle, I get the following:
No genetic map is specified: using 1 cM = 1 Mb
reference samples: 54 target samples: 1
Window 1 [ 22:16050075-18097225 ] reference markers: 50000 target markers: 15625
Imputation time (this window): 1 second
Window 2 [ 22:18012550-19677319 ] reference markers: 50000 target markers: 20700
Imputation time (this window): 0 seconds
Window 3 [ 22:19590416-21408487 ] reference markers: 50000 target markers: 19438
Imputation time (this window): 0 seconds
Window 4 [ 22:21326470-23114729 ] reference markers: 50000 target markers: 20139
Imputation time (this window): 0 seconds
Window 5 [ 22:23049637-24461942 ] reference markers: 50000 target markers: 6498
Imputation time (this window): 0 seconds
ERROR: Reference and target files have no markers in common in interval: 22:24335363-25915693
Common markers must have identical CHROM, POS, REF, and ALT fields. Exiting program.
I appreciate any help thet I can get.
Thanks in advance,
Jadiel A. Colón
