Entering edit mode
2.1 years ago
g.wang2
▴
10
Hi there,
I'm wondering if you may have encountered a similar issue below when using bcftools to re-annotate SNP IDs?
Example code:
./bcftools annotate -c ID -a 00-All.vcf.gz -Oz -o chr8_re-annotated.vcf.gz chr8.vcf.gz
I have tried to re-annotate some regions on chr2, 4, 8, 16 and 19. This has been successful for chr2, 4 and 16 but the command line above hung when it came to chr8 and 19. I had to terminate the run and noted the re-annotated vcf.gz files for chr8 and 19 have 'unexpected end of file'.
I would appreciate any views you have on this.
Guan
run
gunzip -t 00-All.vcf.gzandgunzip -t chr8.vcf.gzto test your input files...Thanks Pierre, I've just checked and both files passed integrity check. The per-chr vcf files were generated in one go before, and have been used for other analyses such as SNPTEST2 with no error. I'm puzzled with the current annotation run.
Some details are not clear to me, but if you terminated your
bcftools annotatecommand while it was still running then writing of the results to the output filechr8_re-annotated.vcf.gzwill have been interrupted resulting in an improperly formatted file. So it makes sense that downstream tasks that usechr8_re-annotated.vcf.gzas input would throw this 'unexpected end of file' error which is indicating a formatting issue.Sorry, I see it's confusing.
Basically, the command line run on chr8 just hung there after some time (the new file size was not increasing any more). It didn't seem to finish after a long while, so I terminated it.
The same command line for chr2,4,16 run smoothly. I haven't been able to figure out why.
Just to add, I first filtered these chromosomes with bcftools prior to annotation (INFO>0.3 and MAF>0.05). These chromosomes were processed consistently at each step.