Check chromosome name: error

I'm trying to use add_hom_refs_to_vcf.pl tool to add hom ref to a VCF file. I'm getting errors about chromosome names and I made changes according to the errors but I still get errors. Here is the errors and how I tried to debug them:
1- Error: Check chromosome name: ##fileformat=VCFv4.0
1- Debugging: I removed configs that were not 1-23.
2- I got the error again
2- Debugging: I added "chr" to the start of chromosome numbers.
3- I got the error again.
3- Debugging: I deleted VCF file header
4- Error changed to: Could not parse the fileformat version string [#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE], assuming VCFv4.2
Check chromosome name: OM
5- I removed Hash sign:
5- Could not parse the fileformat version string [CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE], assuming VCFv4.2
Broken VCF header, no column names?

I can't figure out what the issue is. My VCF is standard and I've used with other tools before. Any help would be appreciated.

[findingdan]

not sure... do you have the string "OM" appear somewhere in your VCF file?

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On Mon, Jan 2, 2023 at 2:21 AM Azjer2014 ***@***.***> wrote: I'm trying to use add_hom_refs_to_vcf.pl tool to add hom ref to a VCF file. I'm getting errors about chromosome names and I made changes according to the errors but I still get errors. Here is the errors and how I tried to debug them: 1- Error: Check chromosome name: ##fileformat=VCFv4.0 1- Debugging: I removed configs that were not 1-23. 2- I got the error again 2- Debugging: I added "chr" to the start of chromosome numbers. 3- I got the error again. 3- Debugging: I deleted VCF file header 4- Error changed to: Could not parse the fileformat version string [#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE], assuming VCFv4.2 Check chromosome name: OM 5- I removed Hash sign: 5- Could not parse the fileformat version string [CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE], assuming VCFv4.2 Broken VCF header, no column names? I can't figure out what the issue is. My VCF is standard and I've used with other tools before. Any help would be appreciated. — Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXAWYAM5OMR4FABGEPZXTDWQJ6WVANCNFSM6AAAAAATOSSQAI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

It's the last two letters of CHROM in the header.

[findingdan]

gotcha, so yea so i bet that implies that the first line should have a # character, and the genomic location chromosome should be prefixed by "chr"

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On Sat, Jan 21, 2023 at 6:59 PM Azjer2014 ***@***.***> wrote: It's the last two letters of CHROM in the header. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXAWYHIYP3LRL4CBGJ5SQDWTRZ7TANCNFSM6AAAAAATOSSQAI> . You are receiving this because you commented.Message ID: ***@***.***>

Thank you! I will try this. The header did have # but it probably was not the first line.

[findingdan]

it's probably gotta be the first character of the first line, try that it's been a long time since i looked at that code but if that's still not working and you still want to use this code email me all the code you're using and the files it runs on and any example files on the github and i'll take a look at this again

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On Sat, Jan 21, 2023 at 7:21 PM Azjer2014 ***@***.***> wrote: Thank you! I will try this. The header did have # but it probably was not the first line. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAXAWYGHSPL2PI7IXXI5Q4DWTR4RLANCNFSM6AAAAAATOSSQAI> . You are receiving this because you commented.Message ID: ***@***.***>