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Errors when using samtools faidx and bgzip for indexing human reference genome

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

bgzip samtools
• 5,712 views • link
updated by Ram Ram • written by hello_bioinf • hello_bioinf

GRCh38_latest_genomic.fa is already compressed.

Just test this with

file GRCh38_latest_genomic.fa

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

If you download it then it is a gzipped file already. So save it as *.fa.gz. Then use gzip -d to decompress, then recompress with bgzip.

• 0 views • link
written by ATpoint ATpoint

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