how to transfer SNV file to plink format

Question

[LZhang]

I got SNV file, and need to transfer to Plink data format. This file is not like SNP file with single mutation.

SNV   SNP_ID  Ref_Allele      Alt_Allele      Chrs    Position        S1      S2      S3      S4 ...
SNV00500        rs3805454       G       A       5       170241168       G/G     G/A     A/A     G/G
SNV00501        rs3833483       GTGTGCGTGC      -       6       36076345-36076354       GTGTGCGTGC/-    GTGTGCGTGC/-    GTGTGCGTGC/GTGTGCGTGC   GTGTGCGTGC/GTGTGCGTGC
SNV00502        rs61236346      -       ATT     4       185549857-185549857     -/ATT   -/-     -/-     -/ATT
SNV00503        rs145823343     -       T       3       132420504-132420504     -/T     -/-     -/-     -/T
SNV00504        rs8175  A       G       4       114682566       A/A     A/A     A/A     A/G
SNV00505        rs11354576      C       -       7       30792057-30792057       C/-     C/C     C/-     C/C
...

As you can file, some of Position is not one, and Ref Allele is not single, also there are "-" in Allele, how can I transfer to Plink ? Should I transfer these multiple letters to single one, e.g for SNV00501, should I transfer "GTGTGCGTGC" to "I", and "-" to "D", then also update Samples info in S1-S4 ...? How to deal with Position location to plink map file as well?

Thanks for help. Any suggestion would be appreciated.

Best

[colindaven]

Doesn't look like a standard format at all. I reckon you'll have to try a custom python script or similar. Happy hacking and good luck.