You're using incompatible versions of samtools and bcftools. If you use bcftools 1.1 or 1.2, then you'll want to use samtools 1.1 or 1.2. If you really want to continue using samtools 0.1.19, then use that version of bcftools.
Devon -- Devon Ryan, Ph.D. Email: [email protected] Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Tue, May 19, 2015 at 3:32 AM, Wei Quan Low <[email protected]> wrote: > Dear experts, > > I entered the command: > samtools mpileup -u aln2.bam.s.bam | bcftools view -vcg - | vcfutils.pl > vcf2fq > aln2.fq > > However this error keeps popping up : > [vcf.c:759 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is > supported. > > May I know where the error is being thrown from. > > SAMtools 0.1.19-44428cd > > bcftools: used both 1.2 (using htslib 1.2.1) and 1.1 (using htslib 1.1) > > I searched online and they mentioned this has already been fixed but I guess > not? > > Thank you all for your time > > ------------------------------------------------------------------------------ > One dashboard for servers and applications across Physical-Virtual-Cloud > Widest out-of-the-box monitoring support with 50+ applications > Performance metrics, stats and reports that give you Actionable Insights > Deep dive visibility with transaction tracing using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
