Hello, I am trying to run the fixref plugin found here, to correct for snpflip errors in my topmed imputation. I found this code here: https://samtools.github.io/bcftools/howtos/plugin.fixref.html
for i in {1..22}
do
bcftools norm --check-ref e -f $OUTDIR/DAC14_send_to_topmed/Homo_sapiens_assembly38_withchrfa.fa $OUTDIR/DAC14_send_to_topmed/DAC14_chr$i\_hg38_nonduplicates.vcf.gz -Ou -o /dev/null
As my build is hg38 and I need to keep the chr prefix in my reference file, I decided to use the GATK HG38 Build called: Homo_sapiens_assembly38.fasta found here: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0;tab=objects?prefix=&forceOnObjectsSortingFiltering=false
I keep receiving this error message:
Failed to load the fai index: /sc/arion/projects/psychgen2/MAP2_dac/data/imputation/DAC14_send_to_topmed/Homo_sapiens_assembly38_withchr.fasta [E::fai_build_core] Format error, unexpected "<" at line 2
I cannot seem to find the solution to this error.