Closed mcolpus closed 10 months ago
It is not invalid, it just means the indel did not survive the calling step, there was not enough support for the indel. If run as bcftools call -mA
, the considered alternate alleles will not be removed, even when unused. If run with -mv
, such lines will not show up at all.
I'm using
bcftools mpileup
andcall
to align long read nanopore data. It produces some odd lines in the resulting vcf like pos 2528:It's called it an indel but provided no ALT. However, looking In the pileup there is an ALT:
So it seems like
bcftools call
determines that the indel is low quality, but only half removes it. I'm not even sure if the resulting line is valid for vcf?What's going on here? Is this expected behaviour.
commands: