What does this bcf error mean?
0
votes
1
answer
775
views
I ran this code to filter out biallelic variants from my vcf file:
bcftools view --max-alleles 2 --exclude-types indels merged.ecDNA.vcf.gz>merged.ecDNA2.vcf.gz
However, I got an error message:
[E::vcf_parse_format] Number of columns at 1:219048632 does not match the number of samples (111 vs 231)
Error: VCF parse error
The thing is,
merged.ecDNA2.vcf.gz
still appeared in my directory and it seems to be a working vcf file. So I was wondering, if my code actually produced a vcf file that appears to be normally functioning, would the above error still have any effect on my output file?
What should the number 1:219048632
refer to?
I tried this code too:
bcftools view -m2 -M2 -v snps merged.ecDNA.vcf.gz>merged.ecDNA3.vcf.gz
And I got the same error message for the above code.
If anyone could give a general explanation of what that error message means, it would be super helpful.
Asked by Michelle Yang
(25 rep)
Aug 9, 2021, 04:47 AM
Last activity: Feb 16, 2022, 05:29 AM
Last activity: Feb 16, 2022, 05:29 AM