Dear all,
I am making a consensus.fa
from a aligned.bam
using bcftools consensus
.
cat reference.fa | bcftools consensus calls.vcf.gz > consensus.fa
The generated consensus.fa
only contains parts of chr1 and I get the following error:
The site chr1:724953 overlaps with another variant, skipping...
The site chr1:797380 overlaps with another variant, skipping...
The fasta sequence does not match the REF allele at chr1:1298836:
.vcf: [CAGAG]
.vcf: [CAG] <- (ALT)
.fa: [GAGAG]TTTTGTTCTTTTGCTCAGGATGGAGAGCAGTGGTGCAATC
I double checked: the reference.fa is hg19
, and the bam
is aligned to hg19
, too.
I am appreciating if someone has any suggestions how to solve this issue.
Robert
Hello RobertUt ,
was the same
reference.fa
used for alignment?This doesn't explain your problem. But before creating the consensus, I strongly recommend to normalize your vcf file, by using
bcftools norm
.fin swimmer
Hi fin,
might be a curious question: What do you normalize your
vcf file
for? Because I don't see how normalizing would have helped to solve my problem.Ut