depth of coverage total summary should not be 100.0
Answered
REQUIRED for all errors and issues:
a) GATK version used: v4.1.9.0
b) Exact command used:
$GATK --java-options "-Xmx"$memory"G -XX:ParallelGCThreads=$thread" DepthOfCoverage -R $GENOME_FASTA -O $BQSR_DIR/"$pid" -I $BQSR_DIR/recal_reads.bam -gene-list $genelist -L $CBED --summary-coverage-threshold 1 --summary-coverage-threshold 5 --summary-coverage-threshold 10 --summary-coverage-threshold 20 --summary-coverage-threshold 50 --output-format TABLE -RF MappingQualityReadFilter --minimum-mapping-quality 20
c) Entire program log:
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx160G -XX:ParallelGCThreads=44 -jar /gpfs/shared/WES_analyses/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar DepthOfCoverage -R /gpfs/shared/WES_analyses/refs/refs/broad_human_bundle_hg37/Homo_sapiens_assembly19.fasta -O pid -I recal_reads.bam -gene-list /gpfs/shared/WES_analyses/Annotations/hg19/GeneList-refseq/hg19_refSeq-gene-transcript-list.refseq -L /gpfs/shared/WES_analyses/bedfiles/FBN1.bed --summary-coverage-threshold 1 --summary-coverage-threshold 5 --summary-coverage-threshold 10 --summary-coverage-threshold 20 --summary-coverage-threshold 50 --output-format TABLE -RF MappingQualityReadFilter --minimum-mapping-quality 20
10:19:53.562 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/shared/WES_analyses/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 10, 2022 10:19:53 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:19:53.849 INFO DepthOfCoverage - ------------------------------------------------------------
10:19:53.849 INFO DepthOfCoverage - The Genome Analysis Toolkit (GATK) v4.1.9.0
10:19:53.850 INFO DepthOfCoverage - For support and documentation go to https://software.broadinstitute.org/gatk/
10:19:53.850 INFO DepthOfCoverage - Executing as sselvi@server001.mesten.local on Linux v3.10.0-1062.12.1.el7.x86_64 amd64
10:19:53.850 INFO DepthOfCoverage - Java runtime: IBM J9 VM v8.0.5.30 - pxa6480sr5fp30-20190207_01(SR5 FP30)
10:19:53.850 INFO DepthOfCoverage - Start Date/Time: May 10, 2022 10:19:53 AM TRT
10:19:53.850 INFO DepthOfCoverage - ------------------------------------------------------------
10:19:53.850 INFO DepthOfCoverage - ------------------------------------------------------------
10:19:53.850 INFO DepthOfCoverage - HTSJDK Version: 2.23.0
10:19:53.850 INFO DepthOfCoverage - Picard Version: 2.23.3
10:19:53.850 INFO DepthOfCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:19:53.851 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:19:53.851 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:19:53.851 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:19:53.851 INFO DepthOfCoverage - Deflater: IntelDeflater
10:19:53.851 INFO DepthOfCoverage - Inflater: IntelInflater
10:19:53.851 INFO DepthOfCoverage - GCS max retries/reopens: 20
10:19:53.851 INFO DepthOfCoverage - Requester pays: disabled
10:19:53.851 WARN DepthOfCoverage -
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: DepthOfCoverage is a BETA tool and is not yet ready for use in production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
10:19:53.851 INFO DepthOfCoverage - Initializing engine
10:19:54.310 INFO FeatureManager - Using codec BEDCodec to read file file:///gpfs/shared/WES_analyses/bedfiles/FBN1.bed
10:19:54.318 INFO IntervalArgumentCollection - Processing 8616 bp from intervals
10:19:54.322 INFO DepthOfCoverage - Done initializing engine
10:19:54.341 INFO ProgressMeter - Starting traversal
10:19:54.341 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
10:19:54.492 INFO FeatureManager - Using codec BEDCodec to read file file:///gpfs/shared/WES_analyses/bedfiles/FBN1.bed
10:19:54.499 INFO FeatureManager - Using codec RefSeqCodec to read file file:///gpfs/shared/WES_analyses/Annotations/hg19/GeneList-refseq/hg19_refSeq-gene-transcript-list.refseq
10:19:54.510 WARN Utils - **********************************************************************
10:19:54.510 WARN Utils - * WARNING:
10:19:54.510 WARN Utils - *
10:19:54.510 WARN Utils - * RefSeq file contains transcripts with zero coding length. Such
10:19:54.510 WARN Utils - * transcripts will be ignored (this warning is printed only once)
10:19:54.510 WARN Utils - **********************************************************************
10:19:59.609 INFO DepthOfCoverage - 0 read(s) filtered by: WellformedReadFilter
26861 read(s) filtered by: NotDuplicateReadFilter
39 read(s) filtered by: NotSecondaryAlignmentReadFilter
48 read(s) filtered by: MappedReadFilter
3 read(s) filtered by: MappingQualityReadFilter
26951 total reads filtered
10:19:59.609 INFO ProgressMeter - chr15:48829927 0.1 8616 98132.1
10:19:59.610 INFO ProgressMeter - Traversal complete. Processed 8616 total loci in 0.1 minutes.
10:19:59.611 INFO DepthOfCoverage - Outputting summary info
10:19:59.614 INFO DepthOfCoverage - Outputting locus summary
10:19:59.619 INFO DepthOfCoverage - Shutting down engine
[May 10, 2022 10:19:59 AM TRT] org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=137822208
Tool returned:
success
Hello,
While I calculate per gene coverage I realized that there is a gap in the first exon and the gap is correctly calculated in the interval summary table. But the total coverage summary of the gene is 100.0. I should not get 100.0 coverage of the whole target region if there are any missing bases.
The results as below.
Interval summary:
Target total_coverage average_coverage S19_total_cvg S19_mean_cvg S19_granular_Q1 S19_granular_median S19_granular_Q3 S19_%_above_1 S19_%_above_5 S19_%_above_10 S19_%_above_20 S19_%_above_50
chr15:48703187-48703576 168310 431.56 168310 431.56 371 420 481 100.0 100.0 100.0 100.0 100.0
chr15:48704766-48704940 123182 703.90 123182 703.90 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48707733-48707964 150308 647.88 150308 647.88 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48712884-48713003 54684 455.70 54684 455.70 427 453 >500 100.0 100.0 100.0 100.0 100.0
chr15:48713755-48713883 74644 578.64 74644 578.64 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48714149-48714265 60312 515.49 60312 515.49 456 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48717566-48717688 82444 670.28 82444 670.28 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48717936-48718061 98343 780.50 98343 780.50 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48719764-48719970 115961 560.20 115961 560.20 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48720543-48720668 63455 503.61 63455 503.61 497 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48722868-48722999 88043 666.99 88043 666.99 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48725063-48725185 118305 961.83 118305 961.83 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48726791-48726910 61338 511.15 61338 511.15 466 490 >500 100.0 100.0 100.0 100.0 100.0
chr15:48729158-48729274 108669 928.79 108669 928.79 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48729519-48729584 26474 401.12 26474 401.12 339 404 468 100.0 100.0 100.0 100.0 100.0
chr15:48729965-48730114 87624 584.16 87624 584.16 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48733918-48734043 59477 472.04 59477 472.04 443 468 >500 100.0 100.0 100.0 100.0 100.0
chr15:48736738-48736857 52580 438.17 52580 438.17 413 451 475 100.0 100.0 100.0 100.0 100.0
chr15:48737573-48737701 66969 519.14 66969 519.14 433 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48738903-48739019 90231 771.21 90231 771.21 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48740965-48741090 66648 528.95 66648 528.95 498 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48744759-48744881 87275 709.55 87275 709.55 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48748834-48748959 109969 872.77 109969 872.77 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48752443-48752514 28718 398.86 28718 398.86 368 407 429 100.0 100.0 100.0 100.0 100.0
chr15:48755279-48755437 114026 717.14 114026 717.14 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48756096-48756218 109096 886.96 109096 886.96 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48757765-48757890 71158 564.75 71158 564.75 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48757987-48758055 34796 504.29 34796 504.29 462 475 >500 100.0 100.0 100.0 100.0 100.0
chr15:48760135-48760299 129660 785.82 129660 785.82 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48760609-48760731 61293 498.32 61293 498.32 470 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48762831-48762953 60234 489.71 60234 489.71 434 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48764748-48764873 103767 823.55 103767 823.55 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48766452-48766574 101950 828.86 101950 828.86 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48766725-48766847 46653 379.29 46653 379.29 367 376 398 100.0 100.0 100.0 100.0 100.0
chr15:48773852-48773977 78042 619.38 78042 619.38 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48776015-48776140 88218 700.14 88218 700.14 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48777571-48777693 94453 767.91 94453 767.91 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48779272-48779397 51197 406.33 51197 406.33 353 418 480 100.0 100.0 100.0 100.0 100.0
chr15:48779509-48779634 66185 525.28 66185 525.28 448 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48780310-48780438 55701 431.79 55701 431.79 366 402 >500 100.0 100.0 100.0 100.0 100.0
chr15:48780565-48780690 49408 392.13 49408 392.13 371 387 422 100.0 100.0 100.0 100.0 100.0
chr15:48782048-48782275 121655 533.57 121655 533.57 481 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48784658-48784783 76276 605.37 76276 605.37 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48786401-48786451 33544 657.73 33544 657.73 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48787320-48787457 127530 924.13 127530 924.13 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48787666-48787785 63313 527.61 63313 527.61 487 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48788297-48788422 120898 959.51 120898 959.51 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48789463-48789588 77311 613.58 77311 613.58 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48791182-48791235 26428 489.41 26428 489.41 485 497 >500 100.0 100.0 100.0 100.0 100.0
chr15:48795984-48796136 152973 999.82 152973 999.82 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48797222-48797344 84957 690.71 84957 690.71 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48800779-48800901 98669 802.19 98669 802.19 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48802241-48802366 74695 592.82 74695 592.82 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48805746-48805865 76210 635.08 76210 635.08 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48807584-48807724 78284 555.21 78284 555.21 500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48808380-48808559 40869 227.05 40869 227.05 203 233 254 100.0 100.0 100.0 100.0 100.0
chr15:48812856-48813014 139907 879.92 139907 879.92 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48818327-48818452 115316 915.21 115316 915.21 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48826277-48826402 46697 370.61 46697 370.61 241 347 >500 100.0 100.0 100.0 100.0 100.0
chr15:48829808-48830005 119703 604.56 119703 604.56 488 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48888480-48888575 62173 647.64 62173 647.64 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48892336-48892431 97493 1015.55 97493 1015.55 >500 >500 >500 100.0 100.0 100.0 100.0 100.0
chr15:48902925-48903023 45311 457.69 45311 457.69 396 456 >500 100.0 100.0 100.0 100.0 100.0
chr15:48905207-48905289 21594 260.17 21594 260.17 243 259 277 100.0 100.0 100.0 100.0 100.0
chr15:48936803-48936966 38410 234.21 38410 234.21 162 287 313 98.2 98.2 98.2 97.6 90.9
Sample summary
sample_id total mean granular_third_quartile granular_median granular_first_quartile %_bases_above_1 %_bases_above_5 %_bases_above_10 %_bases_above_20 %_bases_above_50
S19 5300016 615.14 500 500 465 100.0 100.0 100.0 100.0 99.8
Total 5300016 615.14 N/A N/A N/A N/A N/A N/A N/A N/A
IGV screenshot
Thank you for highlighting this issue
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Thank you for your post, Sinem Selvi! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi Sinem Selvi,
Thanks for writing into the forum so that we can look into this issue! I have a couple notes from our developer team that you can consider:
- DepthofCoverage only handles exons and won't penalize gaps of coverage that occur in an intron.
- The tool traverses the gene in intervals and so if this gap is in between those traversal intervals, the tool might miss a gap in coverage.
- What does the interval list you are using look like?
Please let us know if this applies to your situation so that we can better understand what you are seeing.
Best,
Genevieve
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Hello,
Thank you to consider the issue. The coverage covers the exon. You can find the interval list below. The gap occurred in the first exon of the interval list (chr15:48936802-48936966).chr15 48703186 48703576 461_282669_2200(FBN1)_66 0 -
chr15 48704765 48704940 461_282668_2200(FBN1)_65 0 -
chr15 48707732 48707964 461_282667_2200(FBN1)_64 0 -
chr15 48712883 48713003 461_282666_2200(FBN1)_63 0 -
chr15 48713754 48713883 461_282665_2200(FBN1)_62 0 -
chr15 48714148 48714265 461_282664_2200(FBN1)_61 0 -
chr15 48717565 48717688 461_282663_2200(FBN1)_60 0 -
chr15 48717935 48718061 461_282662_2200(FBN1)_59 0 -
chr15 48719763 48719970 461_282661_2200(FBN1)_58 0 -
chr15 48720542 48720668 461_282660_2200(FBN1)_57 0 -
chr15 48722867 48722999 461_282659_2200(FBN1)_56 0 -
chr15 48725062 48725185 461_282658_2200(FBN1)_55 0 -
chr15 48726790 48726910 461_282657_2200(FBN1)_54 0 -
chr15 48729157 48729274 461_282656_2200(FBN1)_53 0 -
chr15 48729518 48729584 461_282655_2200(FBN1)_52 0 -
chr15 48729964 48730114 461_282654_2200(FBN1)_51 0 -
chr15 48733917 48734043 461_282653_2200(FBN1)_50 0 -
chr15 48736737 48736857 461_282652_2200(FBN1)_49 0 -
chr15 48737572 48737701 461_282651_2200(FBN1)_48 0 -
chr15 48738902 48739019 461_282650_2200(FBN1)_47 0 -
chr15 48740964 48741090 461_282649_2200(FBN1)_46 0 -
chr15 48744758 48744881 461_282648_2200(FBN1)_45 0 -
chr15 48748833 48748959 461_282647_2200(FBN1)_44 0 -
chr15 48752442 48752514 461_282646_2200(FBN1)_43 0 -
chr15 48755278 48755437 461_282645_2200(FBN1)_42 0 -
chr15 48756095 48756218 461_282644_2200(FBN1)_41 0 -
chr15 48757764 48757890 461_282643_2200(FBN1)_40 0 -
chr15 48757986 48758055 461_282642_2200(FBN1)_39 0 -
chr15 48760134 48760299 461_282641_2200(FBN1)_38 0 -
chr15 48760608 48760731 461_282640_2200(FBN1)_37 0 -
chr15 48762830 48762953 461_282639_2200(FBN1)_36 0 -
chr15 48764747 48764873 461_282638_2200(FBN1)_35 0 -
chr15 48766451 48766574 461_282637_2200(FBN1)_34 0 -
chr15 48766724 48766847 461_282636_2200(FBN1)_33 0 -
chr15 48773851 48773977 461_282635_2200(FBN1)_32 0 -
chr15 48776014 48776140 461_282634_2200(FBN1)_31 0 -
chr15 48777570 48777693 461_282633_2200(FBN1)_30 0 -
chr15 48779271 48779397 461_282632_2200(FBN1)_29 0 -
chr15 48779508 48779634 461_282631_2200(FBN1)_28 0 -
chr15 48780309 48780438 461_282630_2200(FBN1)_27 0 -
chr15 48780564 48780690 461_282629_2200(FBN1)_26 0 -
chr15 48782047 48782275 461_282628_2200(FBN1)_25 0 -
chr15 48784657 48784783 461_282627_2200(FBN1)_24 0 -
chr15 48786400 48786451 461_282626_2200(FBN1)_23 0 -
chr15 48787319 48787457 461_282625_2200(FBN1)_22 0 -
chr15 48787665 48787785 461_282624_2200(FBN1)_21 0 -
chr15 48788296 48788422 461_282623_2200(FBN1)_20 0 -
chr15 48789462 48789588 461_282622_2200(FBN1)_19 0 -
chr15 48791181 48791235 461_282621_2200(FBN1)_18 0 -
chr15 48795983 48796136 461_282620_2200(FBN1)_17 0 -
chr15 48797221 48797344 461_282619_2200(FBN1)_16 0 -
chr15 48800778 48800901 461_282618_2200(FBN1)_15 0 -
chr15 48802240 48802366 461_282617_2200(FBN1)_14 0 -
chr15 48805745 48805865 461_282616_2200(FBN1)_13 0 -
chr15 48807583 48807724 461_282615_2200(FBN1)_12 0 -
chr15 48808379 48808559 461_282614_2200(FBN1)_11 0 -
chr15 48812855 48813014 461_282613_2200(FBN1)_10 0 -
chr15 48818326 48818452 461_282612_2200(FBN1)_9 0 -
chr15 48826276 48826402 461_282611_2200(FBN1)_8 0 -
chr15 48829807 48830005 461_282610_2200(FBN1)_7 0 -
chr15 48888479 48888575 461_282609_2200(FBN1)_6 0 -
chr15 48892335 48892431 461_282608_2200(FBN1)_5 0 -
chr15 48902924 48903023 461_282607_2200(FBN1)_4 0 -
chr15 48905206 48905289 461_282606_2200(FBN1)_3 0 -
chr15 48936802 48936966 461_282605_2200(FBN1)_2 0 -Thank you for your time.
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Hi @Sinem Selvi thank you for your reply. Looking more closely at your results and your interval list file I'm not sure I fully understand what is wrong if anything with your results thus far. I notice that there is indeed a gap in coverage of a few bases in the vicinity chr15:48936966. However this does indeed to be reflected in the sample_summary output I do indeed see reflected in the last few columns of the last row that there were indeed bases without depth >= 1 covered (the 98.2 reported there. That looks correct to me. I notice that this doesn't seem to be reflected in the sample summary table output at the bottom and its undclear why except to say that it could be that number is getting rounded poorly. It might be worth digging into that if that is the issue here.
I see you have subsequently included the gene-list. I would make 100% sure that the intervals in this gene-list are totally covered by the .bed file you used as your interval list or else there might be missing bases in that 461_282605_2200(FBN1)_2 gene that are resulting in your gene summary file being wrong. I will note however that there is a difference in the output files from DepthOfCoverage in regards to gene-lists. Specifically when you include a --gene-list input to the tool you should see files named "...sample_gene_summary" which should have gene specific data which does not look like the output file that you listed in your initial post. Hopefully that does reflect the dropoff in coverage correctly for the gene in question? If not I would make sure the bed intervals are complete. Thank you. -
Hello James Emery thank you for your answer.
You can see sample_gene_summary result below.
Gene total_coverage average_coverage S19_total_cvg S19_mean_cvg S19_granular_Q1 S19_granular_median S19_granular_Q3 S19_%_above_1 S19_%_above_5 S19_%_above_10 S19_%_above_20 S19_%_above_50
FBN1|NM_000138 5300016 615.14 5300016 615.14 465 >500 >500 100.0 100.0 100.0 100.0 99.8The result is the same as sample_summary table. "99.8" calculation looks correct. But the problem is there is no read in the first bases so, there is no even %5 coverage in the first 3 bases. If we see %100 coverage below 20 reads, we would miss if there is any gap.
Thank you
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Hi @Sinem Selv
Intersting. Its possible there is some rounding going on if there are many bases and the number of uncovered edge bases is under .1% of the overall count of bases, this warrants some thought. However I'm curious what gene you are looking at for FBN1|NM_000138. I don't see it (just its subunits) in the gene-summary list. The coverage information for that gene is suspiciously similar to the overall S1 coverage information. What exactly does your gene list look like? Currently DepthOfCoverage only supports the .refseq gene list format like this:#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
74 NM_033486 chr1 - 1570602 1655859 1571125 1654257 20 1570602,1571298,1571694,1572043,1572258,1572442,1572769,1573123,1573861,1575637,1576408,1577022,1577266,1577746,1643702,1647784,1650766,1653034,1654146,1655705, 1571218,1571488,1571843,1572160,1572366,1572564,1572875,1573245,1573952,1575813,1576474,1577181,1577362,1577869,1643839,1647917,1650894,1653150,1654271,1655859, 0 CDK11B cmpl cmpl 0,2,0,0,0,1,0,1,0,1,1,1,1,1,2,1,2,0,0,-1,
74 NM_033489 chr1 - 1570602 1655859 1571125 1654035 21 1570602,1571298,1571694,1572043,1572258,1572442,1572769,1573123,1573861,1575637,1576408,1577022,1577266,1577746,1643702,1647784,1650766,1653034,1654026,1654146,1655705, 1571218,1571488,1571843,1572160,1572366,1572564,1572875,1573245,1573952,1575813,1576474,1577181,1577362,1577869,1643839,1647917,1650894,1653150,1654073,1654271,1655859, 0 CDK11B cmpl cmpl 0,2,0,0,0,1,0,1,0,1,1,1,1,1,2,1,2,0,0,-1,-1,
74 NM_033490 chr1 - 1570602 1655859 1571125 1577849 19 1570602,1571298,1571694,1572043,1572258,1572442,1572769,1573123,1573861,1575637,1576408,1577022,1577266,1577746,1647784,1650766,1653034,1654146,1655705, 1571218,1571488,1571843,1572160,1572366,1572564,1572875,1573245,1573952,1575813,1576474,1577181,1577362,1577869,1647917,1650894,1653150,1654271,1655859, 0 CDK11B cmpl cmpl 0,2,0,0,0,1,0,1,0,1,1,1,1,0,-1,-1,-1,-1,-1,
74 NM_001787 chr1 - 1570602 1655859 1571125 1654257 20 1570602,1571298,1571694,1572043,1572258,1572442,1572769,1573123,1573861,1575637,1576408,1577022,1577266,1577707,1643702,1647784,1650766,1653034,1654146,1655705, 1571218,1571488,1571843,1572160,1572366,1572564,1572875,1573245,1573952,1575813,1576474,1577181,1577362,1577869,1643839,1647917,1650894,1653150,1654271,1655859, 0 CDK11B cmpl cmpl 0,2,0,0,0,1,0,1,0,1,1,1,1,1,2,1,2,0,0,-1, -
Hello James Emery
It might be rounding as it is small number of bases. But when we work on single genes, total coverage is considered in detail.
I created the gene list from refseq as explained in GATK. The interested gene as below:
#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2|name cdsStartStat cdsEndStat exonFrames
119 NM_000138 chr15 - 48700509 48937906 48703186 48936966 66 48700509,48704765,48707732,48712883,48713754,48714148,48717565,48717935,48719763,48720542,48722867,48725062,48726790,48729157,48729518,48729964,48733917,48736737,48737572,48738902,48740964,48744758,48748833,48752442,48755278,48756095,48757764,48757986,48760134,48760608,48762830,48764747,48766451,48766724,48773851,48776014,48777570,48779271,48779508,48780309,48780564,48782047,48784657,48786400,48787319,48787665,48788296,48789462,48791181,48795983,48797221,48800778,48802240,48805745,48807583,48808379,48812855,48818326,48826276,48829807,48888479,48892335,48902924,48905206,48936802,48937771, 48703576,48704940,48707964,48713003,48713883,48714265,48717688,48718061,48719970,48720668,48722999,48725185,48726910,48729274,48729584,48730114,48734043,48736857,48737701,48739019,48741090,48744881,48748959,48752514,48755437,48756218,48757890,48758055,48760299,48760731,48762953,48764873,48766574,48766847,48773977,48776140,48777693,48779397,48779634,48780438,48780690,48782275,48784783,48786451,48787457,48787785,48788422,48789588,48791235,48796136,48797344,48800901,48802366,48805865,48807724,48808559,48813014,48818452,48826402,48830005,48888575,48892431,48903023,48905289,48937147,48937906, 0 FBN1|NM_000138 cmpl cmpl 0,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,0,-1,
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