Re: [Samtools-help] Problem Picard/GATK

Hi John,

Many Picard programs assume there is a sequence dictionary alongside a 
reference fasta.  For ref.fasta, this would be ref.dict in the same 
directory.  Prior to running ReorderSam, do the following:

java -jar 
/data/results/software/picard-tools-1.47/CreateSequenceDictionary.jar 
REFERENCE=/data/results/genomes/hg18/hg18.fa 
OUTPUT=/data/results/genomes/hg18/hg18.dict

-Alec

On 6/16/11 12:41 PM, john herbert wrote:
>
> 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, does 
> anyone know how to fix this?
>
> Thank you,
>
> John.
>
>
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