Entering edit mode
3.1 years ago
Negin ▴ 20
I used the command below to normalize my vcf file by splitting multiple alternatives into multiple rows:
bcftools norm -m - <in.vcf> > out.vcf
but some of the variants disappeared after normalization!! Does anyone know why this happened?
Can you provide a specific example of disappearing variants?
Here, the example:
Btw, I didn't copy the genotype fields for all the samples.
That's not a complete example: you only stated the input, not the output and what was missing from it. Imagine yourself on the other side of this: what information would you need to reproduce the problem at all? If we can't do that, we can't really help.
Because I can't post a long reply, I show only the variant that was part of the input, but it disappeared from the output. I hope this is helpful. Otherwise, which kind of information do you need?
Can you reproduce the problem by pasting just that line into a VCF file, and then copying over a bunch of header lines? If not, we have no hope; we don't even have access to the header lines which you haven't posted, or the bcftools version, or...