Hi Alessandro, any chance you could provide a small example to reproduce the error?
Best wishes, Petr On Mon, 2015-11-23 at 10:01 +0000, Alessandro Mammana wrote: > Hi all, > > I am trying to filter regions in a vcf file using a bed file. > More precisely, I am trying to add an INFO field like this > 'TARGET=name_of_target_region_from_bed_file' . Additionally, I am > using the same regions to filter the vcf file with the -R option (but > this doesn't really play a role as the segfault happens also without > the -R option). > > This is the command that I am using: > > > bcftools annotate -a tmp_sorted.bed.gz -h header.txt -c > CHROM,FROM,TO,TARGET test.vcf.gz > > Which prints some header lines, some vcf lines and then segfaults. > > The file tmp_sorted.bed is bgzipped and tabindexed and the first > lines look like this: > > chr1 1225899 1226912 target_1 > chr1 12066709 12066788 target_2 > chr1 24687414 24687493 target_3 > > the file header.txt looks like this: > > ##INFO=<ID=TARGET,Number=1,Type=Integer,Description="Closest target > region in the manifest file"> > > the file test.vcf.gz is also bgzipped and tabindexed and it's just a > normal vcf file. > > Do you know what the problem could be? > > Best, > Alessandro Mammana > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 > _______________________________________________ > Samtools-help mailing list > [email protected] > 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. ------------------------------------------------------------------------------ Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
