Hi guys!
I am trying to calculate some metrics with CalculateHsMetrics from Picard,
and I am getting this error:
Exception in thread "main" htsjdk.samtools.SAMException: Query asks for
data past end of contig
at
htsjdk.samtools.reference.IndexedFastaSequenceFile.getSubsequenceAt(IndexedFastaSequenceFile.java:181)
at
picard.analysis.directed.TargetMetricsCollector.<init>(TargetMetricsCollector.java:225)
at
picard.analysis.directed.HsMetricCollector.<init>(HsMetricCollector.java:47)
at
picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:96)
at
picard.analysis.directed.CalculateHsMetrics.makeCollector(CalculateHsMetrics.java:48)
at
picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:108)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
This is my command line:
*java -Xmx8G -jar /opt/picard/picard.jar CalculateHsMetrics
BAIT_INTERVALS=sample_bait_intervals.txt
TARGET_INTERVALS=sample_target_intervals.txt
INPUT=sample.sorted.dedupped.bam OUTPUT=sample_picard_hs_metrics.txt
METRIC_ACCUMULATION_LEVEL=ALL_READS REFERENCE_SEQUENCE=genome.fa
VALIDATION_STRINGENCY=LENIENT*
I obtain my sample_bait_intervals.txt and sample_target_intervals.txt files
like this:
*samtools view -H sample.bam > sample_bam_header.txt*
*cat sample_primary_coord.bed | gawk '{print $1 "\t" $2+1 "\t" $3
"\t+\tinterval_" NR}' > sample_target_body.txt*
*cat sample_bam_header.txt sample_target_body.txt > sample_target_intervals*
And in the same way for *sample_bait_intervals.txt* just taking into
account the *sample_capture_coord.bed* instead of *sample_primary_coord.bed*
Thanks in advance!!
MF
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