Entering edit mode
2.2 years ago
amy__
▴
160
Hello,
I know there are previous questions on this topic, but they have not helped my problem.
I am trying to use samtools faidx to index the human reference genome. I have downloaded the GRCh38 fasta file from here: https://www.ncbi.nlm.nih.gov/genome/guide/human/. I saved it as an .fa file.
When running
samtools faidx GRCh38_latest_genomic.fa
I first get this error:
[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip
[faidx] Could not build fai index GRCh38_latest_genomic.fa.fai
When I do
bgzip GRCh38_latest_genomic.fa
I get this error:
[E::fai_build_core] Format error, unexpected character at line 1
[faidx] Could not build fai index GRCh38_latest_genomic.fa.gz.fai
I need to get a .fai file so that I can use with deepvariant.
Thanks, Amy
GRCh38_latest_genomic.fa is already compressed.
Just test this with
file GRCh38_latest_genomic.fa