freebayes only picking up variants in a single contig
Hi there! I am having a lot of trouble with variant calling with freebayes variant calling. I have a .fa file with a contig for the E. coli reference genome. I also have a contig for Cas9. I run the following code
freebayes-parallel <(fasta_generate_regions.py sequences.fa.fai 100000) 16 -f sequences.fa --ploidy 1 test.bam > test.vcf
It runs perfectly fine but I am not able to see any mutations for the Cas9 contig and only the E. coli reference. I've made sure that my BAM file has reads mapping to both contigs which it does
NC_000913.3 4641652 46281033 0
lcl|Cas9 4104 747006 0
I even looked at the BAM file in IGV and saw regions of Cas9 that have suspected deletions. Any idea what I might be doing wrong here?
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