We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

GATK4 GetPileupSummaries

Hi, I use GATK GetPileupSummaries to estimate contamination, the output has many sites, as in the following picture

so, which sites are used to estimate contamination? can someone point these sites in the picture?

Answers

  • vptvpt Member

    Hi,

    I am getting GetPileupSummaries to complete seemingly without error. But, the output table has no records; it only has a header column. I have tried different steps to resolved, but I have not yet figured out the problem. Below I show the content of the output file and then the content of the error log file. Please let me know if you have any suggestions to get this to work. Thanks.

    $ cat ../output/GetPileupSummaries_sample.table

    SAMPLE=sample

    contig position ref_count alt_count other_alt_count allele_frequency

    $ cat ../logs/GetPileupSummaries_sample.e1687454
    20:50:23.394 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/research/gatk-4.1.1.0/gatk-package-4.1.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    Apr 11, 2019 8:50:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
    INFO: Failed to detect whether we are running on Google Compute Engine.
    20:50:25.075 INFO GetPileupSummaries - ------------------------------------------------------------
    20:50:25.076 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.1.1.0
    20:50:25.076 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
    20:50:25.076 INFO GetPileupSummaries - Executing as [email protected] on Linux v2.6.32-754.6.3.el6.x86_64 amd64
    20:50:25.076 INFO GetPileupSummaries - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_111-b14
    20:50:25.076 INFO GetPileupSummaries - Start Date/Time: April 11, 2019 8:50:23 PM CDT
    20:50:25.076 INFO GetPileupSummaries - ------------------------------------------------------------
    20:50:25.076 INFO GetPileupSummaries - ------------------------------------------------------------
    20:50:25.077 INFO GetPileupSummaries - HTSJDK Version: 2.19.0
    20:50:25.077 INFO GetPileupSummaries - Picard Version: 2.19.0
    20:50:25.077 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    20:50:25.077 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    20:50:25.077 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    20:50:25.077 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    20:50:25.077 INFO GetPileupSummaries - Deflater: IntelDeflater
    20:50:25.077 INFO GetPileupSummaries - Inflater: IntelInflater
    20:50:25.077 INFO GetPileupSummaries - GCS max retries/reopens: 20
    20:50:25.077 INFO GetPileupSummaries - Requester pays: disabled
    20:50:25.077 WARN GetPileupSummaries -

    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    Warning: GetPileupSummaries is a BETA tool and is not yet ready for use in production

    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    20:50:25.077 INFO GetPileupSummaries - Initializing engine
    20:50:25.385 INFO FeatureManager - Using codec VCFCodec to read file file:///research/gatk-test-data__wgs_ubam__HCC1143T/af-only-gnomad.hg38.common.bialleliconly.canonicalonly.sorted.vcf.gz
    20:50:25.476 INFO FeatureManager - Using codec VCFCodec to read file file:///research/gatk-test-data__wgs_ubam__HCC1143T/af-only-gnomad.hg38.common.bialleliconly.canonicalonly.sorted.vcf.gz
    20:50:32.502 INFO IntervalArgumentCollection - Processing 3893864 bp from intervals
    20:50:32.658 INFO GetPileupSummaries - Done initializing engine
    20:50:32.659 INFO ProgressMeter - Starting traversal
    20:50:32.659 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
    20:50:48.040 INFO ProgressMeter - chr1:6440859 0.3 1000 3900.9
    20:50:58.234 INFO ProgressMeter - chr1:109668196 0.4 10000 23460.4
    20:51:09.042 INFO ProgressMeter - chr1:205798757 0.6 18000 29684.2
    20:51:19.522 INFO ProgressMeter - chr2:91657746 0.8 29000 37130.3
    20:51:29.869 INFO ProgressMeter - chr3:11703110 1.0 41000 42999.5
    20:51:40.812 INFO ProgressMeter - chr3:196270152 1.1 53000 46660.4
    20:51:51.152 INFO ProgressMeter - chr5:59609419 1.3 68000 51979.2
    20:52:02.195 INFO ProgressMeter - chr6:32580364 1.5 80000 53609.7
    20:52:12.692 INFO ProgressMeter - chr7:39451383 1.7 93000 55781.6
    20:52:23.402 INFO ProgressMeter - chr8:1973262 1.8 103000 55804.9
    20:52:33.964 INFO ProgressMeter - chr9:92751039 2.0 117000 57870.7
    20:52:44.265 INFO ProgressMeter - chr10:95611086 2.2 129000 58812.4
    20:52:54.806 INFO ProgressMeter - chr11:71481179 2.4 140000 59094.2
    20:53:05.445 INFO ProgressMeter - chr12:66507205 2.5 152000 59691.3
    20:53:15.826 INFO ProgressMeter - chr14:55096987 2.7 165000 60674.0
    20:53:26.302 INFO ProgressMeter - chr15:88120713 2.9 176000 60814.4
    20:53:37.666 INFO ProgressMeter - chr16:71756318 3.1 184000 59673.7
    20:53:48.695 INFO ProgressMeter - chr17:66096036 3.3 194000 59376.8
    20:53:59.211 INFO ProgressMeter - chr19:18222463 3.4 206000 59839.9
    20:54:09.384 INFO ProgressMeter - chr20:31509092 3.6 215000 59522.4
    20:54:19.496 INFO ProgressMeter - chr22:49924664 3.8 226000 59778.9
    20:54:25.935 INFO GetPileupSummaries - 4313566 read(s) filtered by: (((((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
    4313566 read(s) filtered by: ((((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter) AND GoodCigarReadFilter)
    4313566 read(s) filtered by: (((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND MateOnSameContigOrNoMappedMateReadFilter)
    4296314 read(s) filtered by: ((((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
    4296314 read(s) filtered by: (((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
    4296314 read(s) filtered by: ((((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter) AND NotDuplicateReadFilter)
    592640 read(s) filtered by: (((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND PrimaryLineReadFilter)
    583953 read(s) filtered by: ((MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter) AND MappedReadFilter)
    583953 read(s) filtered by: (MappingQualityAvailableReadFilter AND MappingQualityNotZeroReadFilter)
    583953 read(s) filtered by: MappingQualityNotZeroReadFilter
    8687 read(s) filtered by: PrimaryLineReadFilter
    3703674 read(s) filtered by: NotDuplicateReadFilter
    17252 read(s) filtered by: MateOnSameContigOrNoMappedMateReadFilter

    20:54:25.935 INFO ProgressMeter - chrX:143216908 3.9 231568 59560.7
    20:54:25.935 INFO ProgressMeter - Traversal complete. Processed 231568 total loci in 3.9 minutes.
    20:54:25.961 INFO GetPileupSummaries - Shutting down engine
    [April 11, 2019 8:54:25 PM CDT] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 4.04 minutes.
    Runtime.totalMemory()=3227516928
    $

  • xiuczxiucz Member

    Hi,

    I am getting a USER ERROR with WGS data, however ,this error did not occur with WES or PANEL data, because of their bed file, I think. Can you tell me how to avoid this error?

    A USER ERROR has occurred: Argument intervals was missing: Argument 'intervals' is required.
    
    ~/gatk-4.1.0.0/gatk --java-options '-Xmx20G' GetPileupSummaries \
    -I ~/tumor.recalibrated.bam \
    -V ~/small_exac_common_3_hg19.vcf.gz \
    -O tumor.getpileupsummaries.table
    

    Thank you.

  • lituanlituan Member

    @ vpt, did you check the bam to see if the variant in the vcf is covered by any reads

  • lituanlituan Member

    @ xiucz , for WGS data, I think you can try the bed for the WES data, as long as there are enough sites in the output getpileupsummaries.table, the result will be ok

  • vptvpt Member

    @lituan said:
    @ vpt, did you check the bam to see if the variant in the vcf is covered by any reads

    I can check. I assumed there would be at least one since there are almost 4 million variants in the input file.

  • vptvpt Member

    @vpt said:

    @lituan said:
    @ vpt, did you check the bam to see if the variant in the vcf is covered by any reads

    I can check. I assumed there would be at least one since there are almost 4 million variants in the input file.

    Yes, using bedtools intersect, I find that 29,190 sites of this file overlap with the capture region of the exome-sequencing-derived bam file input.

Sign In or Register to comment.