Unable to load index

Question

[mohammedabeddin1]

I am trying to convert .vcf to .fasta using the .fasta reference by using vcf-consensus but I am getting errors. I am unable to get the reference file as faidx location reference to the reference fasta files are generating errors. It would be nice if someone helped me by giving all the steps for converting a .vcf to .fasta file .

I am converting .vcf file to .fasta file for the location Molecular Location: base pairs 166,195,185 to 166,375,987 on chromosome 2 (Homo sapiens Annotation Release 107, GRCh38.p2) using ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz

Answer 1

[GenoMax]

VCF to FASTA

You should be able to index your fasta by using samtools faidx. Something along the lines of

$ samtools faidx human_g1k_v37.fasta.gz

That should generate a human_g1k_v37.fasta.gz.fai file.