Hello All,
I am trying to call SNPs using samtools mpileup command and I continue to get this error:
[E::faidx_fetch_seq] The sequence "NC_000913.3 Escherichia coli str. K-12 substr. MG1655" not found
I have tried several of the suggested solutions elsewhere on the internet to no avail. Any help would be greatly appreciated.
Some background:
I generated sam files with bbmap then coverted to bam files with samtools view. There were then sorted using samtools sort.
The fasta file was indexed with samtools faidx.
current syntax is:
path-to-program/samtools mpileup -v -f ASM584v2.fna -I Sorted.ERR435575.bam > ERR435575.vcf
Please show output of:
meaning to check if this sequene name is present in both the fasta reference and the SAM header.
grep "NC_000913.3 Escherichia coli str. K-12 substr. MG1655" ASM584v2.fna
/path-to-/samtools view -H Sorted.ERR435575.bam