Hi Casper, is both samtools and bcftools version 1.1? For calling, "bcftools call" should be used with new versions instead.
Petr On Thu, 2014-10-09 at 15:44 -0700, Casper Shyr wrote: > Hello, > When executing samtools mpileup I get the error: > > [bcf_sync] incorrect number of fields (6 != 5) at 5387:235995136 > > The command i use is: > samtools mpileup -Bgf hg19-orderMito.fasta IN.sorted.bam | bcftools view > -gvc - > OUT.bcf > The samtools version is 1.1. > The weird part is this command works if I use samtools version 0.1.19. It has > always been working for me, but doesn’t work when I upgrade to version 1.1. > Everything else is the same, same input, same commands. The only difference > is samtools version. - it works right now if I revert back to the older > samtools, but does not work in the new version. > > Anybody else seeing this? What’s different about the new version that makes > me to suddenly have this error? > > Thank you, > Casper > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > _______________________________________________ > 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. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
