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Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

BAIT Interval and Target Interval file format issue.

I'm trying to run CalculateHsMetrics with following command from Picard Tools

java -jar /tools/picard-tools-1.141/picard.jar CalculateHsMetrics \
BI=probe_cancer_panel_2.0.bed \
TI=target_cancer_panel_2.0.bed \
I=R1_edit3_8bp_TE030_fq-quality_checked_R2_edit3_8bp_TE030_fq-quality_checked__sort46.bam \

Getting Following STDOUT:

[Thu Feb 11 15:40:12 IST 2016] picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=[probe_cancer_panel_2.0.bed] TARGET_INTERVALS=[target_cancer_panel_2.0.bed] INPUT=R1_edit3_8bp_TE030_fq-quality_checked_R2_edit3_8bp_TE030_fq-quality_checked__sort46.bam OUTPUT=output 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 GA4GH_CLIENT_SECRETS=client_secrets.json
[Thu Feb 11 15:40:12 IST 2016] Executing as root@pts00256 on Linux 3.16.0-30-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15; Picard version: 1.141(8ece590411350163e7689e9e77aab8efcb622170_1447695087) IntelDeflater
[Thu Feb 11 15:40:12 IST 2016] picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.00 minutes.
To get help, see
Exception in thread "main" java.lang.IllegalStateException: Interval list file must contain header.
at htsjdk.samtools.util.IntervalList.fromReader(
at htsjdk.samtools.util.IntervalList.fromFile(
at htsjdk.samtools.util.IntervalList.fromFiles(
at picard.analysis.directed.CollectTargetedMetrics.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(

I'm not able to understand "Interval list file must contain header."

"probe_cancer_panel_2.0.bed" file used as BAIT file, contents(first 10 lines) as follows :

chr1 17345282 17345332 SDHB|NM_003000_exon_0_0_chr1_17345225_r_1_1939010 1000 +
chr1 17345375 17345425 SDHB|NM_003000_exon_0_0_chr1_17345225_r_0_1939009 1000 -
chr1 17345486 17345536 SDHB|NM_003000_exon_0_0_chr1_17345225_r_1_1939010 1000 -
chr1 17345123 17345173 SDHB|NM_003000_exon_0_0_chr1_17345225_r_0_1939009 1000 +
chr1 17349254 17349304 SDHB|NM_003000_exon_1_0_chr1_17349103_r_0_2563050 1000 -
chr1 17349014 17349064 SDHB|NM_003000_exon_1_0_chr1_17349103_r_0_2563050 1000 +
chr1 17350378 17350428 SDHB|NM_003000_exon_2_0_chr1_17350468_r_0_2563051 1000 +
chr1 17350619 17350669 SDHB|NM_003000_exon_2_0_chr1_17350468_r_0_2563051 1000 -
chr1 17354413 17354463 SDHB|NM_003000_exon_3_0_chr1_17354244_r_0_2563052 1000 -
chr1 17354152 17354202 SDHB|NM_003000_exon_3_0_chr1_17354244_r_0_2563052 1000 +

"target_cancer_panel_2.0.bed" file used as Target file, contents(first 10 lines) as follows :

chr1 1981908 1982140 PRKCZ|NM_002744_exon_0_0_chr1_1981909_f
chr1 1986879 1987001 PRKCZ|NM_002744_exon_1_0_chr1_1986880_f
chr1 1987922 1988012 PRKCZ|NM_002744_exon_2_0_chr1_1987923_f
chr1 1990979 1991030 PRKCZ|NM_002744_exon_3_0_chr1_1990980_f
chr1 2005085 2005368 PRKCZ|NM_001033581_exon_0_0_chr1_2005086_f
chr1 2005424 2005714 PRKCZ|NM_001242874_exon_0_0_chr1_2005425_f
chr1 2036154 2036334 PRKCZ|NM_001033582_exon_0_0_chr1_2036155_f
chr1 2066700 2066786 PRKCZ|NM_001033581_exon_1_0_chr1_2066701_f
chr1 2075648 2075780 PRKCZ|NM_001033581_exon_2_0_chr1_2075649_f
chr1 2077465 2077547 PRKCZ|NM_001033581_exon_3_0_chr1_2077466_f

Please let me understand what kind of header it requires.


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