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Old 04-14-2014, 05:53 PM   #1
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Location: Illinois

Join Date: Mar 2014
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Default Getting Reference Name with Samtools/Picard


I am currently working in Picard, the java version of SAMtools. I am using the queryContained() method to count the number of reads in a BAM file by specified regions. This method requires an int start, int end, and String Name. I assume that the String Name value is the name of the reference sequence(s) in the BAM file. I tested this on a Human Chr20 BAM file from NCBI and found that I only got an output if I used "20" as my string name.

Now here's my question: How can I make Picard check the BAM file for me and print out what the name of the reference sequence(s) is? I've tried incorporating the getReferenceName() method, but when I use it on the Chr20 BAM file, I always get "*" as an output. Here is a rough example of the logic I've tried so far:

SAMFileReader reader = new SAMFileReader(bamFile, index);
SAMFileHeader Bob = reader.getFileHeader();
SAMRecord Jimmy = new SAMRecord(Bob);
String Earl = Jimmy.getReferenceName();

Any help will be greatly appreciated
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Old 04-14-2014, 10:24 PM   #2
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use sequence dictionary to get the list of reference sequences:

for(SAMSequenceRecord ssr:Bob.getSequenceDictionary().getSequences())
System.out.println(ssr.getSequenceName() );
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Old 04-15-2014, 12:45 PM   #3
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Thank you! That was exactly what I was looking for!
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