Dear all, SNP calling with samtools/bcftools used to produce a vcf header section with ##contig lines including all the information found in the input bam's @SQ lines like:
##samtoolsVersion=0.1.19-44428cd ##contig=<ID=Chromosome,length=3573470,md5=70ad67622b2fbd848ead0f6aeeabf9a7> Now with samtools/bcftools-1.0 everything except ID and length seems to be ignored: ##samtoolsVersion=1.0+htslib-1.0 ##contig=<ID=Chromosome,length=3573470> Has this behavior been changed on purpose or is it oversight ? Thanks, Wolfgang ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
