bcftools merged vcf file assigns all variants to one sample
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4 months ago

I've made one vcf file for each of three samples. I then combined them using bcftools, like so:

# Make a list of vcf files to merge
cat "${OUT}/results/variants/vcf_list"

/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/3a7a-10.vcf.gz
/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/MF3.vcf.gz
/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/R507H-FB_S355_L001.vcf.gz

Then merge the list:

bcftools merge -l "${OUT}/results/variants/vcf_list" -Ov -o "${OUT}/results/variants/merge_individuals.vcf"

And index it:

tabix -p vcf "${OUT}/results/variants/merge_individuals.vcf.gz"

The resulting merged vcf appears to have three columns, one for each sample. When I open it in IGV all the variants are assigned to sample 3a7a (see image)

enter image description here

But when I open it in GenomeBrowse I see them assigned correctly to each of the three samples:

enter image description here

I can't work out what's going on? I've uploaded the individual and merged vcf files here. Any help much appreciated

https://1drv.ms/u/s!AvBi5ipmBYfrhr8MPIDUjjYIcMI-rw?e=f8imqR

vcf merge gatk igv bcftools • 132 views
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