I suppose, there aren't any.
Mills_and_1000G_gold_standard.indels.hg19.sites.vcf suggests that the data is based on the 1000 Genomes project, and I presume that the Channel catfish has not been sequenced as comprehensively. At least Ensembl has no Variant database for that organism. Maybe there is a specialized database somewhere, but I fear that you will have to do recalibration based on your own sequencing data.
You can do this e.g. with BBTools approximately like so:
Quality score recalibration (be sure to trim adapters first):
bbmap.sh ref=ref.fa in=reads.fq out=mapped.sam
callvariants.sh in=mapped.sam out=initial.vcf ref=ref.fa ploidy=X
bbduk.sh in=mapped.sam out=recal.sam recalibrate
callvariants.sh in= recal.sam out=final.vcf ref=ref.fa ploidy=X
After unpacking BBTools, you will find more info in the
./docs/guides folder. Make sure that you choose the correct ploidy, since some fishes are polyploid and this catfish species even seems to have a variable ploidy. Ideally, the ploidy exactly from the investigated specimen should be determined, if there are still tissue samples left in the freezer.
If in doubt, I would search the literature for variant calling in fishes. At least for Danio rerio and economically important fishes like salmon, there should be variant data out there - as far as I know also the Atlantic Salmon has a variable ploidy, therefore is probably a suitable template organism.
Thanks for you answer Matthias
Hello Matthias I hope that you're okay.
I'm writing you because I have a problem using bbmap.sh :(
When I try to execute the script I have this error: /home/hayler99/miniconda3/envs/bbtools/bin/bbmap.sh: line 347: java: command not found
I tried to put the PATH in the bashrc but it didn't work, so I don't know what to do.
This is my script: bbmap.sh ref=GCF_001660625.2_IpCoco_1.2_genomic.fna -I pimm1_Pg594_il.fastq.gz -O pimm1_Pg594_il.sam
I hope you can help me :)
I wish you a happy new year.
Thanks and a happy new year to you, too.
You need to check, that
which javareturns the path to the executable. I suppose, you have a Java distribution installed, so it is indeed a problem with
Are you using Bash? Because if you are on MacOS, the default terminal emulator is the Z shell and you would need to put the modified