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Old 05-01-2019, 10:51 AM   #10
questor2010
Junior Member
 
Location: Seattle, WA

Join Date: Mar 2010
Posts: 5
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Quote:
Originally Posted by XeroxHero69 View Post
Thanks so much. I tried this command:

bcftools view -f PASS --threads 8 -r chr9:55252802-55252802 -o 722g.990.SNP.INDEL.chrAll.vcf.gz -O z 722g.990.SNP.INDEL.chrAll.vcf.gz

and it returned:
[W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated

Do you think you could point out what I did wrong?
Edit: I think i see my error, i made it output the data to the same file and now I think i ruined that data file... its only 16.1 kb now
Ouch. Yes - that's the problem. I hope you have another copy readily available. The index file warnings are often caused by file transfers. They transfer first for large files and then have an older timestamp. You can use "touch" to fix that, or reindex, but that takes a long time with large vcf files.
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