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[INFO][Launcher]bim2vcf Exited with failure (-1) #144
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I wrote this for a colleagues years ago. As far as I understand my program only handled bases with one character only. Give me a few minutes, I'll update the code for multiple nucleotides. |
@vicruiser i pushed c81f95b , please tell me if that works. Please not for this kind of deletion T/TA I didn't look at the POS in the VCF. But in the VCF, the position should be shifted https://samtools.github.io/hts-specs/VCFv4.2.pdf
so tell me if you think that the POS is wrong for an INS or a DEL. |
It works now! Thanks. I'm going to check carefully the matter about DEL and INS and I'll get back to you. |
Hi again, I think something is wrong with the generated .vcf but not entirely. This is part of the output.vcf for an insertion:
and for a deletion:
I can see labels that are supposed to be deletions (e.g.: 1:69726:D:3) categorized as insertion (;SVTYPE=INS) and the other way around. The reference allele column in my input.bim is the last one. I don't know if that is the problem or is just a problem with labeling. Additionally, I've run VEP to annotate the .vcf generated with bim2vcf and indeed, something goes wrong with the positions but only for deletions. Output of vep for insertion (well categorized as insertion):
Output of vep for deletion (wrongly categorized as insertion):
So basically, yes, if i'm correct, DEL positions should be shifted. Thanks again. |
@vicruiser Hi again, |
handling DEL or INS is quite difficult for me now. There was a bug because I just use one character to get the reference allele. As a quick fix, The DEL or INS are just skipped without error now. |
Ok, I'll wait for the final update then. Thanks for your time. |
In case someone need it: |
Subject of the issue
bim2vcf experiments severe error.
Your environment
openjdk 11 2018-09-25
OpenJDK Runtime Environment 18.9 (build 11+28)
OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)
/bim2vcf/jdk-11
Steps to reproduce
java -jar jvarkit/dist/bim2vcf.jar -R Homo_sapiens.GRCh38.dna.primary_assembly.fa input.bim
input.bim looks like:
It seems that bim2vcf has problems dealing with alleles that are numbers.
Expected behaviour
To run fine.
Actual behaviour
The text was updated successfully, but these errors were encountered: