Fasta.fai file error

Fasta.fai file error


Hi, I have been struggling with an error in bedtools intersect. The command I am trying to run is as follows

bedtools intersect -a sorted.vcf -b nstd166.GRCh38.variant_call_chr.vcf.gz -wo -sorted  -f 0.8 -r  -g Homo_sapiens_assembly38.fasta.fai 

For some of the files that I am assessing, I don’t get any errors and the output is obtained without issues. But sometimes the error I receive is as follows:

Error: The genome file Homo_sapiens_assembly38.fasta.fai has no valid entries. Exiting.

I have been looking for what could be the cause of the problem and I have seen that this is a quite common failure derived from the genome file structure, which in my case is the following:

chrI  15072421 101 112

While according to the bedtools documentation itself, the structure should be

chrI  15072421
chrII 15279323
chrX  17718854
chrM  13794

My question is, how is it possible that for some of the files I got an output but for some of them I get the error?

Thanks in advance!



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