Alignment bwa and human_g1k_v37.fasta genome, fail to locate the index files

[AsanchezMD]

Hello,

I am trying to do the alignment pipeline from fastq files that I got for whole exome sequence. I first used trim_galore to remove adapaters and I got .fq files. Then I downloaded the human_g1k_v37.fasta genome from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz I uncompressed the file an then I use this command to run the alignment:

bwa mem -R "@RG\tSM:sample1\tID:sample1\tPL:ILLUMINA\tCN:HIHG\tLB:MyRGLibraryName" -M -t 4 ...hg19/human_g1k_v37.fasta ...val_1.fq ...val_2.fq > File.sam

however I get this message "fail to locate the index files" My question is, when using the human_g1k_v37.fasta, do I have to index the fasta file? I thought it was already optimized for the alignment and noting else was needed. Your answer is much appreciated!

[MI773R]

You should always generate index from your downloaded genome before reads mapping.