When I create a standard 6 column bed, picard throws the error:
When I use the same format that was used in 1.139 picard throws this error:
Did something change in the way the command is used?
Code:
Exception in thread "main" htsjdk.samtools.SAMException: Invalid interval record contains 6 fields: chr1 955543 955763 AGRN-6|gc=75 0 +
Code:
Exception in thread "main" java.lang.IllegalArgumentException: Invalid strand field: at htsjdk.samtools.util.IntervalList.fromReader(IntervalList.java:467) at htsjdk.samtools.util.IntervalList.fromFile(IntervalList.java:381) at htsjdk.samtools.util.IntervalList.fromFiles(IntervalList.java:410) at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:85)
Code:
TI= @HD VN:1.4 GO:none SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @SQ SN:chrM LN:16569 chr1 955543 955763 + AGRN-6|gc=75 chr1 957571 957852 + AGRN-7|gc=61.2
Code:
BI= @HD VN:1.4 GO:none SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @SQ SN:chrM LN:16569 chr1 955542 955662 + AGRN_70 chr1 955643 955763 + AGRN_71
Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar /home/cmccabe/Desktop/NGS/picard-tools-1.140/picard.jar CalculateHsMetrics BI=/home/cmccabe/Desktop/NGS/bed/picard/unix_sam_sorted_xgen_baits.bed TI=/home/cmccabe/Desktop/NGS/bed/picard/unix_sam_sorted_xgen_targets.bed I=IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader.bam O=/home/cmccabe/Desktop/NGS/IonXpress_004.R_2015_10_29_13_11_15_user_Proton-32-Lurie_Inh_Disease_151029_newheader_all_IDT.CalculateHSmetrics
Comment