Key Error from REF and ALT fields when running DumpSTR on GangSTR vcf file

[BonnieCSE]

DumpSTR throws KeyError: 'csf1poatct' when running on a GangSTR vcf file (Platinum Genomes pedigree). I noticed the error was due to strings such as ‘csf1poatct,’ ‘d7s820tatc,’ and ‘d8s1179tcta’ in the REF and ALT fields in chr5 pos 149455887, chr7 pos 83789542, and chr8 pos 125907115.

[nmmsv]

Hi Bonnie,
Did we figure this out? I remember you mentioned it before but forgot if it was addressed or not.

[BonnieCSE]

Hi Nima, I don't think we've figured it out yet. I think the Key Errors are related to codis markers? -Bonnie

…

On Thu, Feb 13, 2020 at 10:50 AM Nima Mousavi ***@***.***> wrote: Hi Bonnie, Did we figure this out? I remember you mentioned it before but forgot if it was addressed or not. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#81?email_source=notifications&email_token=ALW3KKWOG6SOIJGVBK5MN6TRCWI6XA5CNFSM4JMMWG7KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELWFS6A#issuecomment-585914744>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALW3KKT5OZESCP4J4INWC7TRCWI6XANCNFSM4JMMWG7A> .

[nmmsv]

O cool I remember now.
If you have the bed file that created this issue can you add it here? That way I can reproduce the error and take it from there!

[BonnieCSE]

Is it ok if I send the vcf file? I can't seem to find the bed file.

chr5_subset.vcf is a subset of chr5 (contains one of the 3 lines that cause the error), and when it is the input vcf for dumpSTR, the error is thrown.
plat_merged_errors.vcf contains all 3 of the lines that cause dumpSTR to throw the Key Error.

chr5_subset.vcf.gz
plat_merged_errors.vcf.gz

[nmmsv]

awesome, thanks! I'll check them out later.