Normalise tab-delimited format to annovar input

Question

[graeme.thorn]

I have a (tab-delimited) list of variants that look like:

1  45332088  45332088  T C
2  58159793  58159793  G GTAAT
3  10046720  10046720  CTTAGTAAG TTTAT
11 108297388 108297388 CTA C
16 89770177  89770177  G C
20 69690935  63690935  TGG CGA

and I want to format it for annotating using annovar. I'm finding that using table_annovar.pl that the SNPs are being annotated correctly (lines 1 and 5 above), but anything more complex than that (the insertion in line 2 and the deletion in 4, and the complex variant in line 3) are not being annotated, and are in the .invalid_input file, as they are not in the .avinput format (which, for instance, for lines 2, 4 and 6 would be in the format

2  58159793  58159793  - TAAT
11 108297388 108297388 TA -
20 69690936  69690936  T C
20 69690938  69690938  G A

Is there a way, using convert_annovar.pl for instance, of normalising the TSV file I have into this format?

Answer 1

[graeme.thorn]

Never mind, fixed it by converting into a VCF(-like) file using this information, and relying on table_annovar.pl -vcfinput to convert it back into the correct form