Hi all, I have problems trying to indexing my VCF file with tabix.
Fist, I transformed my gzipped VCF to a bgzipped one “zcat myvariants.vcf.gz | bgzip -c > myvariants.vcf.bgzip.gz” Then, I ran tabix as follows, “tabix -p vcf myvariants.bgzip.vcf" And everything was fine. But the problem is that when a listed the chromosomes, several were missing. Provided that my genome is highly repetitive, I have an assembly with a lot of scaffolds, 829971, but only 296354 were listed with tabix -l flag. has tabix a limit on the number of chromosomes or scaffolds that can be indexed? Thanks in advance. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
