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  • Picard and GATK

    Dear samtools,
    I am using Picard to re-order human chromosomes since GATK is not able to handle different ordering.

    GATK advises me to use the Picard utility picard-tools-1.47/ReorderSam.jar

    I tried to use issuing;

    java -jar /data/results/software/picard-tools-1.47/ReorderSam.jar I=fastq.sorted.bam O=kayrotypic.bam REFERENCE=/data/results/genomes/hg18/hg18.fa

    An error message is generated as follows;
    [Thu Jun 16 17:11:50 BST 2011] net.sf.picard.sam.ReorderSam INPUT=fastq.sorted.bam OUTPUT=kayrotypic.bam REFERENCE=/data/results/genomes/hg18/hg18.fa ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false TMP_DIR=/tmp/corona VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
    ERROR 2011-06-16 17:11:50 ReorderSam No reference sequence dictionary found. Aborting.

    This confuses me a bit as it says in the documentation that;
    “Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. Runs substantially faster if the input is an indexed BAM file.Version: 1.0”

    This states that it does not use a dictionary. In any case, what is this dictionary? How do I get this to work?


    I downloaded the hg18.fa from GATK site and indexed with samtools faidx.


    Thank you,

    John.

  • #2
    Answer is...

    Use CreateSequenceDictionary.jar

    Comment


    • #3
      The sequence dictionary are those lines in the SAM/BAM file in the header which state what reference names are used and how ling they are. For reordering of the BAM file your old BAM file has to have a valid sequence dictionary in the header ( in SAM they start with the @SQ tag)as the Reorder function only changes the order of the alignments. Only if there is a match between the new reference file and the one of the reference files in the old sequence dictionary it keeps the reads.

      So it seems your BAM file doesnt contain any @SQ tags. You could try to output the header only using samtools -H function to see if there are any Reference sequences specified. You could then write the header to a text file using streaming at the command line (something linke samtools -H Bamfile > headerfile) and add the SQ lines.
      then merge the header and the old SAM file with the reheader function...

      There is definitely a fancier way to do it, but that should work out (in case the SQ tags are the problem)

      Comment


      • #4
        oh, too late...

        Comment


        • #5
          Originally posted by ulz_peter View Post
          oh, too late...
          Hi Peter.
          Thanks for answering anyway. I found a subsequent error anyway :-).

          John.

          Comment


          • #6
            New reference sequence does not contain a matching contig

            Hi all,

            I am trying to use reordersam and I get the error below. I have already made a reference.dict file using CreateSequenceDictionary.jar , and the dictionary is in the folder I am working from (with the mapping.bam and reference.fasta files), so I do not know what this error is about. Any ideas?

            Exception in thread "main" net.sf.picard.PicardException: New reference sequence does not contain a matching contig for s_4_r1(paired)contig1
            at net.sf.picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:215)
            at net.sf.picard.sam.ReorderSam.doWork(ReorderSam.java:97)
            at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
            at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
            at net.sf.picard.sam.ReorderSam.main(ReorderSam.java:76)

            Comment


            • #7
              I also have a problem with ReorderSam.
              The error I get is: New reference sequence does not contain a matching contig for chr1.

              Any help/input appreciated.

              Comment

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