Hello, people.
I'm trying to convert a .sam file to a .vcf file.
Before, I mapped my reads using HISAT2. As a result, I generated a .sam file. Next, using SAMtools I converted my files to .bam file and after in a sorted.bam file.
Now, I'm trying to convert to .vcf using BCFtools1.9.
Before, I indexed I ref genome using SAMtools1.9
samtools-1.9/samtools faidx TriTrypDB-43_LbraziliensisMHOMBR75M2904_Genome.fa
Next, I trying to convert using this command:
bcftools-1.9/bcftools mpileup -Ou -f TriTrypDB-43_LbraziliensisMHOMBR75M2904_Genome.fa.fai MP_SRR1185719.sorted.bam | bcftools-1.9/bcftools call -Ov -m> MP_SRR1185719.vcf
As result:
[E :: fai_build_core] Format error, unexpected "L" at line 1
I searched here in Biostar more about this error, and I've tried a lot of sugestions, but I only failed.
At fisrt time, I thought that my reference genome was corrupted but I downloaded it again and insisted on the same error.
What else I can try to resolve that?
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1996luanabianca •
I believe the -f flag needs to be the fasta file, not the fai.
The format fa.fai meaning that the file was indexed. If I use only file.fa, my terminal got unnormal like this.
Try setting the -o option rather than redirecting to a file.
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