one-off error in error message "has invalid alternative characters"

[HenriettaHolze]

Hi, I got following error message:

02:20:12 [WARN] Variant at chr7:148807387 has invalid alternative characters. This record will be ignored.

My vcf file contains following lines:

chr7    148807385       .       C       A       .       PASS    AD=0;DP=167;OTH=0
chr7    148807386       .       A       C       .       PASS    AD=0;DP=173;OTH=0
chr7    148807387       .       A       C       .       PASS    AD=0;DP=212;OTH=0
chr7    148807388       .       G       N       .       PASS    AD=1;DP=233;OTH=0
chr7    148807389       .       T       A       .       PASS    AD=0;DP=245;OTH=0

This suggests that the error message has a one-off error itself.

Best,
Henrietta

[HenriettaHolze]

The same one-off error seems to apply to the --out-variants file.

[pmarks]

Hi Henrietta, That is bizarre. Is there any chance that the character in the file is actually not a simple ASCII character, but some other unicode character that happens to look like a C? If you could subset your VCF to include just these records, check that it still causes the same errors, then send me that VCF I could figure out what's going wrong. Cheers, Pat

…

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[HenriettaHolze]

In the vcf file you can see that the alternative variant for 148807387 is C which is valid but it's N (invalid) for 148807388. 148807388 is not reported in the log file as having an invalid alternative character.
When I compare the positions in the input vcf file and --out-variants file, they match if I add 1 to all positions in the --out-variants file.
I'm pretty sure it is a one-off error. As long as I set the rownames of the output matrices with the input vcf file and not the --out-variants file, this is not impacting the functionality of vartrix.

I'm running VarTrix v1.1.22, installed via conda.