I am having trouble with Picard and have tried many things but hopefully am closer now. I have sorted and indexed the TI= and BI= bed files and removed the @PG from the Ion Torrent bam file using the command below:
Example of TI=
Example of BI=
and here is the error in Picard:
I apologize for the long post, just trying to be thorough. Thank you .
Code:
samtools view -H Input.bam | sed '/^@PG/d' | samtools reheader - Input.bam > Input_newheader.bam
Code:
chr1 955542 955763 + chr1:955542-955763 chr1 957570 957852 + chr1:957570-957852 chr1 976034 976270 + chr1:976034-976270 chr1 976542 976787 + chr1:976542-976787 chr1 976847 977092 + chr1:976847-977092
Code:
chr1 133573 133692 chr1:133573-133692 chr1 659937 660056 chr1:659937-660056 chr1 809529 809649 chr1:809529-809649 chr1 955542 955662 chr1:955542-955662 chr1 955643 955763 chr1:955643-955763
Code:
picard-tools CalculateHsMetrics BI=sort_index_5column_xgen_probes.bed TI=sort_index_5column_xgen_targets.bed I=IonXpress_009_150603_newheader.bam O=IonXpress_009_150603_all_IDT.CalculateHSmetrics[Fri Jun 26 08:32:55 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=sort_index_5column_xgen_probes.bed TARGET_INTERVALS=sort_index_5column_xgen_targets.bed INPUT=IonXpress_009_150603_newheader.bam OUTPUT=IonXpress_009_150603_all_IDT.CalculateHSmetrics TMP_DIR=/tmp/dnascopev VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Fri Jun 26 08:32:55 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=61079552 Exception in thread "main" java.lang.IllegalStateException: Interval list file must contain header. at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:176) at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152) at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83) at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158) at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
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