Complete this survey about your research needs and be entered to win an Amazon gift card or FireCloud credit.
Read more about it here!
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.6 is out. See the GATK4 beta page for download and details.

Likely bug in DiagnoseTargets caused by target regions with no covering reads

TimHughesTimHughes Member
edited April 2013 in Ask the GATK team

I have run both Picard's CalculateHsMetrics.jar and DiagnoseTargets on several VCF files.

For most files both work fine and generate output for all targets.

For some files, DiagnoseTargets does not output stats for certain target regions. CalculateHsMetrics.jar, however, does output stats for all targets. Inspecting the output of these two programs, I see that the regions missing from the DiagnoseTargets output are the regions with 0 coverage in CalculateHsMetrics.jar.

I include some examples of the output here.

java -Xmx8G -jar ${basedir}/cardioBRCA/sw/picard-tools-1.79/CalculateHsMetrics.jar \
VALIDATION_STRINGENCY=STRICT \
BAIT_INTERVALS=$bait \
TARGET_INTERVALS=$target \
REFERENCE_SEQUENCE=${ref} \
I=${filename}.bwasw.valid.bam \
O=${filename}.bwasw.valid.metrics_hsSummary.txt \
PER_TARGET_COVERAGE=${filename}.bwasw.valid.metrics_hsPerTrgt.txt

Part of the CalculateHsMetrics.jar output

14  23851247    23851274    28  MYH6_NM_002471_exon_37_r    0.428571    554.857143  1.663222
14  23851635    23851773    139 MYH6_NM_002471_exon_36_r    0.589928    491.05036   1.471957
14  23852432    23852531    100 MYH6_NM_002471_exon_35_r    0.58    0   0 <<<<<<<<<<<<<<<<<<<
14  23853649    23853928    280 MYH6_NM_002471_exon_34_r    0.628571    513.946429  1.540589
14  23854123    23854252    130 MYH6_NM_002471_exon_33_r    0.561538    115 0.34472
14  23855135    23855342    208 MYH6_NM_002471_exon_32_r    0.644231    309.754808  0.928511
14  23855522    23855834    313 MYH6_NM_002471_exon_31_r    0.603834    129.939297  0.389502
14  23856736    23856864    129 MYH6_NM_002471_exon_30_r    0.55814 182.248062  0.546301
14  23856965    23857134    170 MYH6_NM_002471_exon_29_r    0.564706    237.305882  0.711341
14  23857362    23857549    188 MYH6_NM_002471_exon_28_r    0.558511    340.595745  1.020959
14  23858066    23858266    201 MYH6_NM_002471_exon_27_r    0.646766    375.860697  1.126668
14  23858600    23858722    123 MYH6_NM_002471_exon_26_r    0.585366    167.252033  0.501349
14  23858800    23858930    131 MYH6_NM_002471_exon_25_r    0.572519    214.221374  0.642143
14  23859264    23859657    394 MYH6_NM_002471_exon_24_r    0.649746    173.642132  0.520504
14  23861769    23861863    95  MYH6_NM_002471_exon_23_r    0.442105    340.968421  1.022076
14  23862119    23862268    150 MYH6_NM_002471_exon_22_r    0.526667    495.926667  1.486574
14  23862549    23862729    181 MYH6_NM_002471_exon_21_r    0.519337    679.243094  2.036077
14  23862873    23863119    247 MYH6_NM_002471_exon_20_r    0.518219    332.951417  0.998045
14  23863275    23863534    260 MYH6_NM_002471_exon_19_r    0.573077    454.580769  1.362637
14  23865491    23865631    141 MYH6_NM_002471_exon_18_r    0.602837    196.014184  0.587566
14  23865901    23866028    128 MYH6_NM_002471_exon_17_r    0.523437    661.734375  1.983594
14  23866170    23866291    122 MYH6_NM_002471_exon_16_r    0.639344    268.901639  0.806051
14  23866377    23866468    92  MYH6_NM_002471_exon_15_r    0.51087 302.141304  0.905689
14  23866750    23866824    75  MYH6_NM_002471_exon_14_r    0.56    326.666667  0.979206
14  23867935    23868248    314 MYH6_NM_002471_exon_13_r    0.550955    322.041401  0.965341
14  23869463    23869637    175 MYH6_NM_002471_exon_12_r    0.508571    70.44   0.211149
14  23869916    23870188    273 MYH6_NM_002471_exon_11_r    0.578755    335.534799  1.005788
14  23871671    23871813    143 MYH6_NM_002471_exon_10_r    0.58042 237.993007  0.7134
14  23871904    23872011    108 MYH6_NM_002471_exon_9_r 0.574074    47.046296   0.141024
14  23872555    23872657    103 MYH6_NM_002471_exon_8_r 0.514563    172.640777  0.517502
14  23872922    23872989    68  MYH6_NM_002471_exon_7_r 0.5 164.926471  0.494378
14  23873503    23873599    97  MYH6_NM_002471_exon_6_r 0.618557    369.969072  1.109008
14  23873918    23874033    116 MYH6_NM_002471_exon_5_r 0.551724    220.146552  0.659904
14  23874307    23874338    32  MYH6_NM_002471_exon_4_r 0.53125 515.5   1.545246
14  23874430    23874590    161 MYH6_NM_002471_exon_3_r 0.596273    560.937888  1.68145
14  23874834    23874981    148 MYH6_NM_002471_exon_2_r 0.560811    109.851351  0.329287
14  23876230    23876434    205 MYH6_NM_002471_exon_1_r 0.565854    315.595122  0.946018
14  23882061    23882082    22  MYH7_NM_000257_exon_38_r    0.5 0   0 <<<<<<<<<<<<<<<<<<
14  23882966    23883104    139 MYH7_NM_000257_exon_37_r    0.618705    237.856115  0.71299

DiagnoseTargets command line:

java -Xmx8G -jar $gatk \
-T DiagnoseTargets \
-R $ref \
-o ${filename}.bwasw.valid.metrics_diagTrgts.vcf \
-I ${filename}.bwasw.valid.bam \
-L $target \
-S STRICT \
--minimum_coverage 10 \
--minimum_base_quality 0 \
--minimum_mapping_quality 0

Part of the DiagnoseTargets output (truncated lines for readability)

14  23851247    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23851635    .   A   <DT>    .   EXCESSIVE_COVERAGE  
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Missing output
14  23853649    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23854123    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23855135    .   A   <DT>    .   PASS    
14  23855522    .   A   <DT>    .   PASS    
14  23856736    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23856965    .   A   <DT>    .   PASS    
14  23857362    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23858066    .   A   <DT>    .   PASS    
14  23858600    .   A   <DT>    .   PASS    
14  23858800    .   G   <DT>    .   PASS    
14  23859264    .   A   <DT>    .   BAD_MATE;LOW_MEDIAN_DEPTH;POOR_QUALITY  
14  23861769    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23862119    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23862549    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23862873    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23863275    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23865491    .   A   <DT>    .   PASS    
14  23865901    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23866170    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23866377    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23866750    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23867935    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23869463    .   A   <DT>    .   LOW_COVERAGE    
14  23869916    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23871671    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23871904    .   A   <DT>    .   PASS    
14  23872555    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23872922    .   A   <DT>    .   EXCESSIVE_COVERAGE  
14  23873503    .   A   <DT>    .   PASS    
14  23873918    .   A   <DT>    .   PASS    
14  23874307    .   A   <DT>    .   PASS    
14  23874430    .   A   <DT>    .   PASS    
14  23874834    .   A   <DT>    .   PASS    
14  23876230    .   A   <DT>    .   EXCESSIVE_COVERAGE  
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Missing output should be NO_READS
14  23882966    .   A   <DT>    .   PASS

Best Answer

Answers

  • BTW, just wanted to say thanks for the DiagnoseTargets tool.

    The only functionality I miss are the target names and the GC content. But I can get these from CalculateHsMetrics.jar.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Tim,

    I'll forward this to the developer of DiagnoseTargets, @Carneiro. I'm sure he'll be interested in your feedback, and he'll be able to confirm whether this is a bug or whether the completely uncovered targets are left out on purpose. He may also consider adding the target names and GC content to the output table, since it would be more convenient to have a single tool to do everything.

    Can you just confirm for me that you're running a recent version of the GATK, preferably one of the 2.4 series?

  • The data I provided above was obtained with GATK 2.4-3

  • Hi @Carneiro

    Any news on this?

    Tim :)

Sign In or Register to comment.