Failed to extract FI index.

[miaoxm2]

Hi,

I am currently trying to use this amazing tool to assign reads of offspring pool-seq according to parental variants.
But I am encountering an error at the first step 'prepare genome' attached below.
The pipeline I used is simply : SNPsplit_genome_preparation --reference_genome ref/ --vcf_file pair08.chr19.recode.vcf --strain She1-F08 --strain2 She1-M08 --dual_hybrid --nmasking --full_sequence

But the vcf generated from GATK and filtered using bcftools do not provide a field called 'FI'. I've tried every step from the example vcf file record, there's no field of 'FI'. Is there any way I could generate this format?

By the way, I also tried manually adding this field and calling all my variants as passed "1". It works but it is not the appropriate way of using this tool.

I have one more question afterwards after assigning reads with genome 1 or 2. I would like to count the number of reads fit to both haplotypes in specific regions of genome. Would you perhaps inform me if there's any tools to do that?

Thanks!

Best,
Xiaomeng

[FelixKrueger]

I think the best way forward would be send me the first few lines of your VCF file to take a look? Maybe via email?

Cheers, Felix