Variant Calling with Multiple Individuals in Freebayes

Question

[Laurence]

Hello,

I am currently a new student in Bioinformatics and was trying to do variant calling with Freebayes software. I have 10 individuals and also have a reference genome. I have already sorted and indexed all my .bam files ready for variant calling. I am able to successfully produce a .vcf output file for each individual with target information.

I want to run the freebayes script in order to perform variant calling on all 10 individuals simultaneously and produce one .vcf output file containing information from all 10 individuals. At this point I am quite lost and was hoping for some direction. Below is the code I use for Freebayes piped with a filter. More specifically, I am hoping to compare number of SNPs and allele frequency between the 10 individuals.

freebayes -f ref.fa aln.bam | vcffilter -f "QUAL > 20" >results.vcf

Any help would be much appreciated!

[size_t]

try this:

freebayes -f ref.fa -L bamlist --ploidy 2 --vcf result.vcf

-L : A file containing a list of BAM files to be analyzed.

or

freebayes -f ref.fa aln1.bam aln2.bam aln3.bam ...

Answer 1

[Ming Tommy Tang]

It looks like you can provide multiple bam files and output a gVCF file https://github.com/freebayes/freebayes#usage