[Samtools-help] collectHsMetrics BAIT_INTERVALS file format and input options

Discussion:

Richard Corbett

2012-05-07 18:08:05 UTC

Hi.

Is it possible to run collectHSMetrics without providing both the
BAIT_INTERVALS and TARGET_INTERVALS ? We're trying some new kits but
I don't have the target intervals information for them all, while I do
have the bait_intervals.

Also, what is the format of the expected BAIT_INTERVALS file? I have a
"bed" format file (ie. chr start end), but I'm getting the error below
about header lines missing. I tried sticking in 1 header line leading
with a "#", but that didn't help.

thanks,
RIchard

java -jar CalculateHsMetrics.jar BI=intervals.bed I=HS3059.bam
O=HS3059.bam.out R=human.fasta PER_TARGET_COVERAGE=PTC.txt

[Mon May 07 10:54:27 PDT 2012]
net.sf.picard.analysis.directed.CalculateHsMetrics
BAIT_INTERVALS=/home/nthiessen/exome_sequencing/SureSelect_All_Exon_G3362_with_names.bed
TARGET_INTERVALS=/home/nthiessen/exome_sequencing/SureSelect_All_Exon_G3362_with_names.bed
INPUT=HS3059_2_lanes_dupsFlagged.bam
OUTPUT=HS3059_2_lanes_dupsFlagged.bam.out
REFERENCE_SEQUENCE=/home/pubseq/genomes/9606/hg18/bwa_ind/genome/human.fasta
PER_TARGET_COVERAGE=PTC.txt METRIC_ACCUMULATION_LEVEL=[ALL_READS]
VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
CREATE_MD5_FILE=false
[Mon May 07 10:54:27 PDT 2012] Executing as ***@xhost10.bcgsc.ca on
Linux 2.6.18-194.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_05-b13
[Mon May 07 10:54:27 PDT 2012]
net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time:
0.00 minutes.
Runtime.totalMemory()=757530624
Exception in thread "main" java.lang.IllegalStateException: Interval
list file must contain header.
at
net.sf.picard.util.IntervalList.fromReader(IntervalList.java:193)
at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:169)
at
net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:117)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
at
net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:89)

Alec Wysoker

2012-05-07 18:35:00 UTC

Permalink

Hi Richard,

The file format is described here:

http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html

I think you can supply the same file for BAIT_INTERVALS and
TARGET_INTERVALS if you only have bait intervals.

-Alec

Post by Richard Corbett
Hi.
Is it possible to run collectHSMetrics without providing both the
BAIT_INTERVALS and TARGET_INTERVALS ? We're trying some new kits but
I don't have the target intervals information for them all, while I do
have the bait_intervals.
Also, what is the format of the expected BAIT_INTERVALS file? I have a
"bed" format file (ie. chr start end), but I'm getting the error below
about header lines missing. I tried sticking in 1 header line leading
with a "#", but that didn't help.
thanks,
RIchard
java -jar CalculateHsMetrics.jar BI=intervals.bed I=HS3059.bam
O=HS3059.bam.out R=human.fasta PER_TARGET_COVERAGE=PTC.txt
[Mon May 07 10:54:27 PDT 2012]
net.sf.picard.analysis.directed.CalculateHsMetrics
BAIT_INTERVALS=/home/nthiessen/exome_sequencing/SureSelect_All_Exon_G3362_with_names.bed
TARGET_INTERVALS=/home/nthiessen/exome_sequencing/SureSelect_All_Exon_G3362_with_names.bed
INPUT=HS3059_2_lanes_dupsFlagged.bam
OUTPUT=HS3059_2_lanes_dupsFlagged.bam.out
REFERENCE_SEQUENCE=/home/pubseq/genomes/9606/hg18/bwa_ind/genome/human.fasta
PER_TARGET_COVERAGE=PTC.txt METRIC_ACCUMULATION_LEVEL=[ALL_READS]
VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
CREATE_MD5_FILE=false
Linux 2.6.18-194.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_05-b13
[Mon May 07 10:54:27 PDT 2012]
0.00 minutes.
Runtime.totalMemory()=757530624
Exception in thread "main" java.lang.IllegalStateException: Interval
list file must contain header.
at
net.sf.picard.util.IntervalList.fromReader(IntervalList.java:193)
at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:169)
at
net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:117)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
at
net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:89)
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Richard Corbett

2012-05-07 18:37:54 UTC

Permalink

OK. One part solved. Just needed an actual bed header like this:
track name=targets description="a bunch of regions that are targeted"

Maybe I can do the analysis using a list of baits, and the full list of
exons (a la UCSC or something similar). If this works the way I think
it will, it would enable comparison between bait sets from different
vendors.

thanks,
RIchard