Entering edit mode
4.9 years ago
evelyn
▴
230
Hello Everyone,
I created gvcf files using bcftools:
bcftools mpileup -Ov --gvcf 0 -f ref.fa example.sorted.bam | bcftools call -m --gvcf 0 -o example.vcf
I excluded variants other than SNPs using:
bcftools view --exclude-types indels,mnps,bnd,other example.vcf -o example_1.vcf
Then I want to merge gvcf files using bcftools:
bcftools merge --file-list sample.txt -g ref.fa -O v -o merge.vcf
But it is not working. I am getting an error like Failed to merge alleles
. I am not sure if I am using correct commands. Thank you so much for your help and time!
Is this the whole error message? If not, please post also the rest.
Thanks a lot.
fin swimmer
Hello,
I got:
I checked the block with this position in individual gvcf file:
In IGV, this position has the following information,
Hello again,
could you please try to run
bcftools norm
on all your individual gvcf files before merging?You could also run a check if the REF alleles are set correct:
fin swimmer
Hello, Thank you! I used your suggestion and it got merged without error. However, I am still trying to understand the call symbols for each sample after merging. Here is a snippet of the merged file:
However, I am not able to interpret the symbols here for each sample call. For example, at position 778, for sample_1, there are no reads in IGV so it gave ./.:. but for sample_2, there are reads and calls same as the reference and it gives ./.:0. I could not find any document to understand these symbols so that I can make a better sense of the merged file.
Additionally, for POS 3435, sample_1 has 38 reads same as reference but it calls ./.:0:. I will appreciate your help. Thank you!
Hello evelyn ,
could you please post the vcf lines of the individual gvcf's overlapping the pos 778?
Thanks.
fin swimmer
Hello finswimmer,
Here are the individual lines including POS 778: