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
