perl script to encode vcf in sweep finder format

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Oct 12, 2020, 8:36:44 AM10/12/20

to OmegaPlus

Hi,

I have the same issue with sweeD that some people, with error on the vcf file :

ERROR: There are 63 nucleotides in line 1047. Expected 64 (according to the first SNP in line 1016).

SweeD: SweeD_Input.c:2916: readLine_VCF: Assertion `j==*SNP_SZ' failed.

So i m looking for a script to convert VCF in sweep finder format.

Thanks

karine

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Oct 12, 2020, 1:20:33 PM10/12/20

to OmegaPlus

This assertion suggests that there is something wrong with the input file rather than SweeD.

More specifically, line 1047 most probably does not have the same number of genotype fields as the rest of the file.