Closed:Whole Genome Sequence Imputation with Beagle 4.0

Question

[Wietje]

Hello fellow Biostars,

I am struggling with the imputation of 777k-data to WGS-level in Beagle 4.0. The data preparation worked fine so far and I have a large reference group available (N>400 animals) to impute 44 individuals. The process was completed without warning but when I look into the VCF-files and do a quick comparison some oddities appear...

• the SNP-ID from the 777k-dataset disappear (there were no IDs obvisouly in the WGS-dataset)
• the bases for allele 1 and 2 switch sometimes; in other cases it looks like a strand flip

just a short example (left = 777k data; right = WGS data)

7   10880   BovineHD0700000001 A    C    ## 7   10880   .   A   C

7   33543   BovineHD0700000002  A   G    ## 7   33543   .   G   A

7   43673   BovineHD0700000003  G   A    ## 7   43673   .   G   A

7   49151   BovineHD0700000005  A   G    ## 7   49151   .   T   C

7   53313   BovineHD0700000006  A   G    ## 7   53313   .   A   G

7   83740   BovineHD0700000012  G   A    ## 7   83740   .   C   T

Do you have any idea how this can happen or if I did something wrong? I used default settings in Beagle, no pedigree option invoked. Thanks!