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Question about picard BuildBamIndex
Currently, I have been using Picard's built-in library "BuildBamIndex" in order to index my bam files.
I have followed the manual described in Picard sites but I got error message.
Here is my command line that you can easily understand as below.
java -Xmx8g -XX:ParallelGCThreads=8 -jar $picard/BuildBamIndex.jar I=$RealignedBamDir/$output6
I tried different approach to avoid this error message so I used "samtools index" which i think is also same function as Picard BuildBamIndex.
After using samtools, I successfully got my bam index files.
I suppose that there are no major difference between Picard bamindex and samtools bam index.
I am confusing that why only samtools index procedure is working fine?
Below is my error message when run "BuildBamIndex" from Picard.
**[Sun Jan 18 22:15:42 KST 2015] picard.sam.BuildBamIndex INPUT=/DATA1/sclee1/data/URC_WES/U01/01U_N_Filtered_Sorted_Markdup_readgroup.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Sun Jan 18 22:15:42 KST 2015] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Exception creating BAM index for record HSQ-2K:530:C5PJAACXX:6:2109:18806:13902 1/2 101b aligned read.
Caused by: htsjdk.samtools.SAMException: BAM cannot be indexed without setting a fileSource for record HSQ-2K:530:C5PJAACXX:6:2109:18806:13902 1/2 101b aligned read.
... 6 more
I look forward to hearing positive answers from you soon.