Hi Ying, the error message is perhaps a bit confusing, but gives a useful hint: the -f, --fasta-ref parameter to the fixref plugin is the reference sequence in the fasta format, not a VCF
Best wishes, Petr On Thu, 2017-04-13 at 22:01 +0000, Jin, Ying wrote: > Dear Samtools Support, > > When I submit the following command I got the following error > messages: > > bcftools +fixref GWA1MHCregionforHRC.vcf.gz -Ov -o > GWA1MHCregionforHRCfixref.vcf -- -d -f All_20151104.vcf.gz > [fai_load] build FASTA index. > [fai_build_core] different line length in sequence '(null)'. > Failed to load the fai index: All_20151104.vcf.gz > > The All_20151104.vcf.gz and the All_20151104.vcf.gz.tbi files were > downloaded based on the information from the fixref plugin webpage: > wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/V > CF/All_20151104.vcf.gz > wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/V > CF/All_20151104.vcf.gz.tbi > > > I re-built the All_20151104.vcf.gz.tbi file using the command: tabix > -p vcf All_20151104.vcf.gz and re-submitted the above command and > still got the same error messages. How should I proceed with this? > > Thank you very much in advance! > > Ying > > Ying Jin, M.D., Ph.D. > Senior Instructor, > Human Medical Genetics and Genomics Program > Department of Pediatrics > University of Colorado School of Medicine > 12800 E. 19th Ave., Rm. 3400, mail stop 8300 > Aurora, CO 80045 USA > > Tel. 303-724-3110 > Fax 303-724-3100 > Email ying....@ucdenver.edu > > > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
