Hi, I am using bwa mem align 454 fasta file to a reference genome and "samtools mpileup -ugf ref.fa 454.bam" to generate the BCF format. However, it throws a core dump error. Does the samtools mpileup (v1.1) required quality information in the bam/sam file? In other words, the alignment step should use fastq file instead of fasta file. The 0.1.x version samtools works fine for this case.
Chien-Chi On 9/23/14, 10:37 AM, "John Marshall" <[email protected]> wrote: >New 1.1 versions of htslib, samtools, and bcftools have been released. >These are minor bug-fix releases, and include the following notable fixes >and new functionality compared to 1.0: > >* Samtools fixmate and flagstat now consider supplementary reads >* Sorting BAM files with thousands of reference contigs now completes in >a reasonable amount of time >* Fixed samtools idxstats when displaying statistics from indices >generated by samtools 0.1.x >* Fixed samtools calmd memory leak >* Samtools fixmate now only adds a template cigar tag (ct:Z) when >requested with -c, and never adds it repeatedly >* Regularised script #! directives as #!/usr/bin/env perl etc >* Fixed DPR annotation in samtools mpileup >* New bcftools convert and plugin commands and annotate --rename-chrs >option >* BCFtools norm performance is improved and now averages QUALs and >accumulates IDs and FILTERs >* Improved bcftools filter expressions, query support for IUPAC ambiguity >codes, and annotate support for genotype fields >* Plugins for bcftools have now moved from annotate to the new plugin >command > >These releases can be found at <http://www.htslib.org/>. Development and >source code of these projects are linked from that web site and can be >found in various Git repositories under <https://github.com/samtools>. >Updates to the htslib.org web site are ongoing. In particular, we have >recently added a sample CRAM workflow: see ><http://www.htslib.org/workflow/#mapping_to_cram>. > >Installing the tools will also install manual pages for them. Once >installed, you should be able to use "man bcftools" etc at your command >line to find details of new commands and functionality. Manual pages are >also available online at <http://www.htslib.org/doc/> and these will soon >be updated to reflect the 1.1 release. > > John > >-- > 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. > >-------------------------------------------------------------------------- >---- >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.clkt >rk >_______________________________________________ >Samtools-help mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ 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
