After I removed the two lines, I have been able to index the bcf file. The geno.TRA.bcf <http://gbnci-abcc.ncifcrf.gov/fileman/temp/1348518/geno.TRA.bcf> was generated by delly for translocation SV and I am not sure why it captured positions in a telomere.
Thank you so much for finding the problem so quickly. Jack ---- Yuelin Jack Zhu On Tue, Aug 23, 2016 at 5:45 AM, John Marshall <j...@sanger.ac.uk> wrote: > On 22 Aug 2016, at 21:15, Yuelin Zhu <yue...@gmail.com> wrote: > > I got Segmentation fault whenever doing bcftools index on the following > file: > > > > http://gbnci-abcc.ncifcrf.gov/fileman/temp/1348518/geno.TRA.bcf > [...] > > > > $ bcftools index geno.TRA.bcf > > Segmentation fault > > Thanks for the bug report. Your file contains a couple of records with a > POS field of 0: > > chrUn_gl000237 0 TRA00075433 N [etc] > chrUn_gl000241 0 TRA00075451 N [etc] > > and it is these that is causing bcftools index to crash. If I remove > those two records, the file can be indexed fine. > > The VCF spec says that POS=0 indicates that the variant record is in a > telomere. Is it intentional that there are a couple of telomeric entries > in your file, or is this perhaps a bug or artefact of the analysis program > in use? > > In any case, (1) bcftools index shouldn't crash and (2) if POS=0 is > meaningful and valid in VCF/BCF files, bcftools needs to handle it. So > we'll fix this, and thanks again for the bug report [1]. > > John > > [1] Which I've filed as https://github.com/samtools/htslib/issues/406 > > -- > 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. >
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