Combine multiple vcf (or gVCF) from Ion Torrent

Question

[pavlidisp]

Dear Biostar Community,

I'm trying to combine multiple vcf or gvcf files from IonTorrent (produced by variant caller plugin) in order to obtain a sample vcf similar to 1000Genome Human project. My goal is to perform popgen analyses. However, it seems that currently there is no such an established pipeline for data produced by IonTorrent. Any help would be really valuable.

kind regards,
pavlos

Answer 1

[Jorge Amigo]

bcftools merge

[pavlidisp]

Hi Jorge,

There are two problems with "bcftools merge":

1. it works only with the vcf and not the gvcf files. However, I think that it's wrong to merge just vcf's since I need also to know whether some individual has the reference alleles.

2. even with gvcfs, the results do not seem to be very correct

pavlos

[Jorge Amigo]

didn't know bcftools merge doesn't work with gvcf files. I can see a workaround by converting gvcf files to vcf using bcftools convert --gvcf2vcf, and then merging them into a single vcf file. would that work for you?