error: reference mismatch!
Closed this issue · 6 comments
Hello,
I am using hg38 as reference but I have this error : "error: reference mismatch!". Although when I used an other version of hg38 I don't have this problem the script is running well.
The only difference I think I have is that in one version the chromosome are annotated as 1, 2, 3 .... and in the other : chr1, chr2, chr3 ...
How can I solve this problem ?
Best regards,
Laura
Hello!
You are correct, TIDDIT wants the chromosomes of your bam and reference fasta to be named in the exact same way. As of now, it is not possible to run TIDDIT if the reference does not match the bam file.
I recommend you to download a reference fasta that matches the annotation of your bam file. This can be a bit tricky, but you will probably need it for your other analyses as well! Did your sequencing facility run alignment for you? Maybe they can deliver the fasta file to you.
Good luck!
//Jesper
Thanks for your reply. I think I didn't explain my problem very well. I did 2 alignements. One with a reference which has chromosomes names 1, 2, 3 .... and the other with a reference which the chromosomes are named chr1, chr2, chr3, .....
When I launch TIDDIT with the first bam alignement and the corresponding fasta reference it works.
But when I launch it with th esecond alignment and its reference (chr1, chr2 ....) it doesn't work. I have the error about mismatch reference even if I am using the reference match the reference (it's the one I used for the alignment).
Thanks for your help. I hope I was more clear.
Laura
Hi,
have you checked out the previous issue #43? They were helped by adding an option
-s chr1,chr15,chr14,chr9,chr2
Fingers crossed!
// Daniel
I see, then I understand =P.
Also, are you running the latest version of TIDDIT? The latest version is 2.2.1; it is more stable then the previous version.
With the latest verison there is no longer any need to use the -s parameter
Thanks a lot. It works now.
how nice! Good luck with your SV detection!