SNVer error: chrome not found in Reference

Question

[anjali.gopal91]

Hi all,

I'm pretty new to bioinformatics, so please bear with me if I'm using incorrect terminology.

I'm trying to perform variant calling on a series of genes (NOT a whole genome). I have a fasta file that has reference sequences for all of these genes, and a series of fastq files for reads. I aligned these reads with Bowtie, got an output BAM file, and (since these are haploid genes) am now trying to use SNVer to perform variant calls.

The fasta file that I'm using for SNVer is the same fasta file that I used to make a bowtie index. However, whenever I run this, I'm getting the following error:

The chrome M=AD_2|ORF_ID=6222|GENE=10743|RhIY8ADG02_15:F02|ORF_SIZE=2901 is not found in Reference

Except I've checked the fasta file in question and the reference sequence (with the same title) is actually there.

Not sure what's going on. Is there some key information I'm missing? Is fasta not the appropriate format? Do I have to do pre-processing of the fasta file before I can pass it through SNVer?

Any help would be much appreciated.

Thanks!

Anjali

[rse]

SNVer generates a pretty big output file as compared to other variant callers. What can be the reason? Too many false positives?

Answer 1

[anjali.gopal91]

Never mind, I fixed this. Turns out my bam file was not sorted.

If anyone else has this error, you can get around it by:

samtools sort [filename].bam [output]