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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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cnvkit loh fails: KeyError: 'chromosome' #1441

Closed anastazie closed 7 years ago

anastazie commented 8 years ago

Hello, I am performing CNV analysis on DNA data. Here is my configuration file:

  - analysis: variant2
    genome_build: hg19
    algorithm:
      mark_duplicates: true
      recalibrate: false
      realign: false
      variantcaller: freebayes
      remove_lcr: false
      aligner: bwa
      svcaller: cnvkit
      coverage_interval: genome
      tools_on: svplots

Analysis fails when cnvkit loh is performed with 

KeyError: 'chromosome'

I upgraded bcbio_nextgen, but it didnt help. Do you have any ideas?

Thanks, Anastassiya

Below is full error log

[2016-06-21T19:44Z] Germline extraction for H929_S4_L001, freebayes
[2016-06-21T19:44Z] multiprocessing: split_variants_by_sample
[2016-06-21T19:44Z] Timing: prepped BAM merging
[2016-06-21T19:44Z] Timing: validation
[2016-06-21T19:44Z] multiprocessing: compare_to_rm
[2016-06-21T19:44Z] Timing: ensemble calling
[2016-06-21T19:44Z] Timing: validation summary
[2016-06-21T19:44Z] Timing: structural variation
[2016-06-21T19:44Z] multiprocessing: detect_sv
[2016-06-21T19:44Z] CNVkit diagram plot
[2016-06-21T19:44Z] Selected test sample H929_S3_L001
[2016-06-21T19:44Z] Skipped records: 0 somatic, 0 depth, 0 homozygous
[2016-06-21T19:44Z] Traceback (most recent call last):
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/bin/cnvkit.py", line 11, in <module>
[2016-06-21T19:44Z]     args.func(args)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1182, in _cmd_loh
[2016-06-21T19:44Z]     for chrom, subarr in variants.by_chromosome())
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/collections.py", line 57, in __init__
[2016-06-21T19:44Z]     self.__update(*args, **kwds)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/_abcoll.py", line 571, in update
[2016-06-21T19:44Z]     for key, value in other:
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1181, in <genexpr>
[2016-06-21T19:44Z]     (chrom, subarr["end"].max())
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 203, in by_chromosome
[2016-06-21T19:44Z]     for chrom, subtable in self.data.groupby("chromosome", sort=False):
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 3778, in groupby
[2016-06-21T19:44Z]     **kwargs)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 1427, in groupby
[2016-06-21T19:44Z]     return klass(obj, by, **kwds)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 354, in __init__
[2016-06-21T19:44Z]     mutated=self.mutated)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 2383, in _get_grouper
[2016-06-21T19:44Z]     in_axis, name, gpr = True, gpr, obj[gpr]
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in __getitem__
[2016-06-21T19:44Z]     return self._getitem_column(key)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
[2016-06-21T19:44Z]     return self._get_item_cache(key)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
[2016-06-21T19:44Z]     values = self._data.get(item)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
[2016-06-21T19:44Z]     loc = self.items.get_loc(item)
[2016-06-21T19:44Z]   File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/indexes/base.py", line 1947, in get_loc
[2016-06-21T19:44Z]     return self._engine.get_loc(self._maybe_cast_indexer(key))
[2016-06-21T19:44Z]   File "pandas/index.pyx", line 137, in pandas.index.IndexEngine.get_loc (pandas/index.c:4154)
[2016-06-21T19:44Z]   File "pandas/index.pyx", line 159, in pandas.index.IndexEngine.get_loc (pandas/index.c:4018)
[2016-06-21T19:44Z]   File "pandas/hashtable.pyx", line 675, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12368)
[2016-06-21T19:44Z]   File "pandas/hashtable.pyx", line 683, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12322)
[2016-06-21T19:44Z] KeyError: 'chromosome'
[2016-06-21T19:44Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command '/usr/local/share/bcbio/anaconda/bin/cnvkit.py loh -t -s /media/nasta/Nasta/Projects/rubicon/samples_sub/work/structural/H929_S3_L001/cnvkit/raw/H929_S3_L001-sort-chromfilter.cns -o /media/nasta/Nasta/Projects/rubicon/samples_sub/work/structural/H929_S3_L001/cnvkit/raw/tx/tmp7PoSJu/H929_S3_L001-sort-loh.pdf /media/nasta/Nasta/Projects/rubicon/samples_sub/work/freebayes/H929_S3_L001-effects-ploidyfix-filter.vcf.gz
Selected test sample H929_S3_L001
Skipped records: 0 somatic, 0 depth, 0 homozygous
Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/bin/cnvkit.py", line 11, in <module>
    args.func(args)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1182, in _cmd_loh
    for chrom, subarr in variants.by_chromosome())
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/collections.py", line 57, in __init__
    self.__update(*args, **kwds)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/_abcoll.py", line 571, in update
    for key, value in other:
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1181, in <genexpr>
    (chrom, subarr["end"].max())
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 203, in by_chromosome
    for chrom, subtable in self.data.groupby("chromosome", sort=False):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 3778, in groupby
    **kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 1427, in groupby
    return klass(obj, by, **kwds)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 354, in __init__
    mutated=self.mutated)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 2383, in _get_grouper
    in_axis, name, gpr = True, gpr, obj[gpr]
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in __getitem__
    return self._getitem_column(key)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
    return self._get_item_cache(key)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
    values = self._data.get(item)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
    loc = self.items.get_loc(item)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/indexes/base.py", line 1947, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/index.pyx", line 137, in pandas.index.IndexEngine.get_loc (pandas/index.c:4154)
  File "pandas/index.pyx", line 159, in pandas.index.IndexEngine.get_loc (pandas/index.c:4018)
  File "pandas/hashtable.pyx", line 675, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12368)
  File "pandas/hashtable.pyx", line 683, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12322)
KeyError: 'chromosome'
' returned non-zero exit status 1
Traceback (most recent call last):
  File "/usr/local/bin/bcbio_nextgen.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.8', 'bcbio_nextgen.py')
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script

  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 1484, in run_script

  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.8-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in <module>
    main(**kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.8-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
    run_main(**kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
    fc_dir, run_info_yaml)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 175, in variant2pipeline
    samples = structural.run(samples, run_parallel, "standard")
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/__init__.py", line 119, in run
    for xs in to_process.values()))
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in __call__
    while self.dispatch_one_batch(iterator):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
    self._dispatch(tasks)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
    job = ImmediateComputeBatch(batch)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in __init__
    self.results = batch()
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
    return apply(f, *args, **kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 211, in detect_sv
    return structural.detect_sv(*args)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/__init__.py", line 138, in detect_sv
    for svdata in caller_fn(items):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 29, in run
    return _cnvkit_by_type(items, background)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 39, in _cnvkit_by_type
    return _run_cnvkit_single(items[0])
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 85, in _run_cnvkit_single
    return _associate_cnvkit_out(ckouts, [data])
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 61, in _associate_cnvkit_out
    ckout = _add_plots_to_output(ckout, data)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 425, in _add_plots_to_output
    loh_plot = _add_loh_plot(out, data)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 537, in _add_loh_plot
    do.run(cmd, "CNVkit diagram plot")
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command '/usr/local/share/bcbio/anaconda/bin/cnvkit.py loh -t -s /media/nasta/Nasta/Projects/rubicon/samples_sub/work/structural/H929_S3_L001/cnvkit/raw/H929_S3_L001-sort-chromfilter.cns -o /media/nasta/Nasta/Projects/rubicon/samples_sub/work/structural/H929_S3_L001/cnvkit/raw/tx/tmp7PoSJu/H929_S3_L001-sort-loh.pdf /media/nasta/Nasta/Projects/rubicon/samples_sub/work/freebayes/H929_S3_L001-effects-ploidyfix-filter.vcf.gz
Selected test sample H929_S3_L001
Skipped records: 0 somatic, 0 depth, 0 homozygous
Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/bin/cnvkit.py", line 11, in <module>
    args.func(args)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1182, in _cmd_loh
    for chrom, subarr in variants.by_chromosome())
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/collections.py", line 57, in __init__
    self.__update(*args, **kwds)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/_abcoll.py", line 571, in update
    for key, value in other:
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 1181, in <genexpr>
    (chrom, subarr["end"].max())
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/gary.py", line 203, in by_chromosome
    for chrom, subtable in self.data.groupby("chromosome", sort=False):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 3778, in groupby
    **kwargs)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 1427, in groupby
    return klass(obj, by, **kwds)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 354, in __init__
    mutated=self.mutated)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py", line 2383, in _get_grouper
    in_axis, name, gpr = True, gpr, obj[gpr]
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 1997, in __getitem__
    return self._getitem_column(key)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2004, in _getitem_column
    return self._get_item_cache(key)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1350, in _get_item_cache
    values = self._data.get(item)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3290, in get
    loc = self.items.get_loc(item)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/pandas/indexes/base.py", line 1947, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/index.pyx", line 137, in pandas.index.IndexEngine.get_loc (pandas/index.c:4154)
  File "pandas/index.pyx", line 159, in pandas.index.IndexEngine.get_loc (pandas/index.c:4018)
  File "pandas/hashtable.pyx", line 675, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12368)
  File "pandas/hashtable.pyx", line 683, in pandas.hashtable.PyObjectHashTable.get_item (pandas/hashtable.c:12322)
KeyError: 'chromosome'
' returned non-zero exit status 1
chapmanb commented 8 years ago

Anastassiya; Sorry about the issue. It seems like something is problematic about the CNS file that feeds into the loh calculation:

/media/nasta/Nasta/Projects/rubicon/samples_sub/work/structural/H929_S3_L001/cnvkit/raw/H929_S3_L001-sort-chromfilter.cns

It should look something like:

chromosome      start   end     gene    log2    probes  weight
chr22   500     15500   -       -3.19287        6       5.16667

Is it possible that file is empty? If so, I checked a fix into development which should skip running it in this case which will hopefully let things continue cleanly. You can upgrade with bcbio_nextgen.py upgrade -u development. Hope this fixes it for you. If not happy to dig more understanding more about the problem cns file.

anastazie commented 8 years ago

Brad, thank you for the fix. I ran analysis and it didn't throw an error. However, now, I am getting very low log2ratio (-16 for all chromosomes).

chromosome  start   end gene    log2    probes  weight
chr1    10000   79137895    AL627309.1,CICP27,DDX11L1,FAM138A,MIR1302-10,OR4F5,OR4G11P,OR4G4P,RNU6-1100P,RP11-34P13.13,RP11-34P13.14,RP11-34P13.15,RP11-34P13.16,RP11-34P13.7,RP11-34P13.8,RP11-34P13.9,WASH7P,AP006222.1,AP006222.2,AL732372.1,CICP7,OR4F29,RP4-669L17.1,RP4-669L17.10,RP4-669L17.2,RP4-669L17.4,RP4-669L17.8,RP5-857K21.15,WBP1LP7,RP5-857K21.1,RP5-857K21.2,RP5-857K21.3,RP5-857K21.4,MTND1P23,RP5-857K21.4,RP5-857K21.5,RP5-857K21.4,CICP3,OR4F16,RNU6-1199P,RP11-206L10.1,RP11-206L10.2,RP11-206L10.3,RP11-206L10.4,RP11-206L10.5,RP11-206L10.9,RP5-857K21.4,WBP1LP6,AL645608.2,AL669831.1,FAM41C,FAM87B,LINC00115,LINC01128,RP11-206L10.10,RP11-206L10.8,RP11-206L10.9,TUBB8P11,AL645608.2,AGRN,AL645608.1,C1orf159,C1orf170,HES4,ISG15,KLHL17,NOC2L,PLEKHN1,RNF223,RP11-465B22.3,RP11-54O7.1,RP11-54O7.10,RP11-54O7.11,RP11-54O7.14,RP11-54O7.16,RP11-54O7.17,RP11-54O7.18,RP11-54O7.2,RP11-54O7.3,SAMD11,RP11-465B22.5,ACAP3,AL645728.1,AL645728.2,AL645728.3,ANKRD65,ATAD3A,ATAD3B,ATAD3C,AURKAIP1,B3GALT6,C1orf233,CCNL2,CDK11A,CDK11B,CPSF3L,DVL1,FAM132A,GLTPD1,GNB1,MIB2,MIR200A,MIR200B,MIR429,MMP23A,MMP23B,MRPL20,MXRA8,NADK,PUSL1,RN7SL657P,RP1-140A9.1,RP1-283E3.4,RP1-283E3.8,RP11-345P4.10,RP11-345P4.6,RP11-345P4.7,RP11-345P4.9,RP11-465B22.8,RP4-758J18.10,RP4-758J18.13,RP4-758J18.2,RP4-758J18.7,RP5-890O3.3,RP5-890O3.9,RP5-902P8.10,RP5-902P8.12,SCNN1D,SDF4,SLC35E2,SLC35E2B,SSU72,TAS1R3,TMEM240,TMEM88B,TNFRSF18,TNFRSF4,TTLL10,TTLL10-AS1,UBE2J2,VWA1,AL513477.1,AL589739.1,AL590822.1,AL590822.2,C1orf222,C1orf86,CALML6,FAM213B,GABRD,HES5,MMEL1,MORN1,PANK4,PEX10,PLCH2,PRKCZ,RER1,RP11-181G12.2,RP11-181G12.4,RP11-181G12.5,RP11-547D24.1,RP11-547D24.3,RP13-436F16.1,RP3-395M20.12,RP3-395M20.2,RP3-395M20.3,RP3-395M20.7,RP3-395M20.8,RP3-395M20.9,RP4-713A8.1,RP4-740C4.5,RP4-740C4.6,RP4-740C4.7,RP4-740C4.8,RP4-740C4.9,RP5-892K4.1,SKI,TMEM52,TNFRSF14,TTC34,RP11-740P5.2,RP11-740P5.3,TTC34,ACTRT2,AL008733.1,LINC00982,PRDM16,PRDM16,RP1-163G9.2,PRDM16,PRDM16,RP11-22L13.1,AL691523.1,ARHGEF16,C1orf174,CCDC27,CEP104,DFFB,LINC01134,LRRC47,MEGF6,MIR551A,PRDM16,RN7SL574P,RP1-286D6.5,RP11-168F9.2,RP11-46F15.2,RP5-1092A11.2,RP5-1092A11.5,SMIM1,TP73,TP73-AS1,TPRG1L,WRAP73,RP13-614K11.1,RP13-614K11.2,RP11-374C13.1,RP5-1166F10.1,RP1-37J18.1,RP1-37J18.2,AJAP1,RP11-542C10.1,RP1-58B11.1,MIR4417,RP11-154H17.1,AL356693.1,ACOT7,AL035406.1,AL356261.1,CHD5,DNAJC11,ESPN,GPR153,HES2,HES3,ICMT,KCNAB2,KLHL21,LINC00337,MIR4252,MIR4689,NOL9,NPHP4,PHF13,PLEKHG5,RNF207,RNU6-731P,RP1-120G22.11,RP1-202O8.2,RP1-202O8.3,RP11-58A11.2,RPL22,TAS1R1,THAP3,TNFRSF25,ZBTB48,RP11-242F24.1,snoU13,CAMTA1,RP11-312B8.1,RP11-312B8.2,CAMTA1,RP11-334N17.1,CAMTA1,RNU1-8P,CAMTA1,CAMTA1-IT1,RP3-453P22.2,CAMTA1,RP4-549F15.1,CAMTA1,RP11-338N10.1,RP11-338N10.2,RP11-338N10.3,CAMTA1,PER3,RP3-467L1.4,RP3-467L1.6,UTS2,VAMP3,CTA-215D11.4,ERRFI1,PARK7,RP11-431K24.1,RP5-892F13.2,TNFRSF9,Y_RNA,RNU1-7P,RP11-431K24.2,RP11-431K24.3,RP11-431K24.4,RN7SL729P,RNU6-991P,RERE,RP11-185B14.1,RP4-633I8.3,RP4-633I8.4,RP5-1115A15.1,RP5-1115A15.2,RPL7P11,RPL7P7,SLC45A1,SNORA77,Y_RNA,ENO1,ENO1-AS1,ENO1-IT1,HMGN2P17,RNU6-304P,RP3-477M7.5,RP3-477M7.6,CA6,RN7SL451P,GPR157,SCARNA16,SLC2A5,SLC2A7,MIR34A,RP3-510D11.1,RP3-510D11.2,H6PD,SPSB1,Z98044.1,RNA5SP40,RP13-392I16.1,RP13-15M17.1,SLC25A33,TMEM201,C1orf200,CLSTN1,PIK3CD,RP11-558F24.2,RP11-558F24.4,RP11-558F24.6,AL590639.1,CTNNBIP1,LZIC,MIR5697,NMNAT1,PGAM1P11,RBP7,RN7SKP269,RNU6-828P,RP11-496H15.2,RP11-807G9.2,RP11-84A14.4,RP11-84A14.5,UBE4B,APITD1,APITD1-CORT,CASZ1,CORT,DFFA,KIF1B,MIR1273D,PEX14,PGD,RN7SL614P,RN7SL721P,RN7SL731P,RNU6-37P,RP4-734G22.3,RP4-736L20.3,RP5-1113E3.3,HSPE1P24,AL713997.1,ANGPTL7,C1orf127,CFL1P6,EXOSC10,MASP2,MTOR,MTOR-AS1,RNU6-537P,RP4-635E18.6,RP4-635E18.7,RP4-635E18.8,SRM,TARDBP,Y_RNA,snoU13,MTOR,RNU6-291P,RPL39P6,MTOR,UBE2V2P3,UBIAD1,RP11-149P14.1,PTCHD2,RP1-69M21.2,AGTRAP,C1orf167,CLCN6,DRAXIN,FBXO2,FBXO44,FBXO6,MAD2L2,MTHFR,NPPA,NPPA-AS1,NPPB,RP11-56N19.5,RP5-934G17.6,KIAA2013,MFN2,MIIP,PLOD1,RN7SL649P,RNU5E-1,RNU5E-4P,RP5-1077B9.5,Y_RNA,RNU6-777P,RP11-426M1.2,TNFRSF8,MIR4632,RP5-1118D24.2,RP5-888M10.2,SNORA59A,SNORA70,TNFRSF1B,VPS13D,DHRS3,RNU6ATAC18P,RP11-474O21.5,AADACL4,RP11-474O21.2,AADACL3,C1orf158,PRAMEF1,PRAMEF12,snoU13,HNRNPCL1,PRAMEF10,PRAMEF11,PRAMEF2,PRAMEF22,PRAMEF4,PRAMEF6,PRAMEF7,RNU6-1072P,RP11-450I1.2,RP11-450I1.4,RP5-845O24.3,RP5-845O24.8,WI2-3308P17.2,HNRNPCP5,PRAMEF23,PRAMEF25,PRAMEF26,PRAMEF6,RP13-221M14.2,RP13-221M14.3,RP13-221M14.4,RP13-221M14.6,WI2-2994D6.1,PRAMEF3,PRAMEF5,PRAMEF8,RNU6-771P,RP11-219C24.8,RP11-248D7.2,PRAMEF13,PRAMEF9,RP11-219C24.10,RP11-219C24.6,PRAMEF16,PRAMEF18,PRAMEF21,XX-FW84067D5.1,PRAMEF14,PRAMEF15,XX-FW84067D5.2,PRAMEF17,PRAMEF19,PRAMEF20,LRRC38,RP4-597A16.2,RP4-597A16.3,AL359771.1,PDPN,RNA5SP41,CTA-520D8.2,PRDM2,SCARNA11,RNU6-1265P,RP11-344F13.1,RP4-704D23.1,KAZN,KAZN,TBCAP2,C1orf195,KAZN,RP1-21O18.3,TMEM51,TMEM51-AS1,AGMAT,AL121992.1,CASP9,CELA2A,CELA2B,CHCHD2P6,CTRC,DDI2,DNAJC16,EFHD2,FBLIM1,FHAD1,PLEKHM2,RNU7-179P,RP11-169K16.4,RP11-169K16.6,RP11-169K16.7,RP11-288I21.1,RP3-467K16.2,RP3-467K16.4,RP3-467K16.7,RP4-680D5.2,RP4-680D5.4,RP4-680D5.8,RP4-680D5.9,RSC1A1,SCARNA21,SLC25A34,TMEM82,C1orf64,CLCNKA,CLCNKB,FAM131C,HSPB7,RP1-134O19.3,RP11-169K16.8,RP11-169K16.9,RP11-5P18.1,RP11-5P18.10,RP11-5P18.3,RP11-5P18.5,SPEN,TBC1D3P6,ZBTB17,snoU13,EPHA2,RP11-276H7.2,RP11-276H7.3,ANO7P1,ARHGEF19,ARHGEF19-AS1,C1orf134,CROCCP3,FBXO42,MT1XP1,NECAP2,RP11-430L17.1,RP4-798A10.2,RSG1,SPATA21,SZRD1,AL021920.1,AL355149.1,CROCC,CROCCP2,CROCCP4,EIF1AXP1,ESPNP,FAM231A,FAM231B,FAM231C,MST1L,MST1P2,NBPF1,RNU1-3,RNU1-4,RP4-798A10.4,RP4-798A10.7,RP5-1182A14.5,RP5-875O13.6,U1,ATP13A2,CROCC,MFAP2,MIR3675,PADI2,RNU1-2,RP1-37C10.3,RP11-108M9.1,RP11-108M9.2,RP11-108M9.4,RP11-108M9.5,RP11-108M9.6,SDHB,U1,Y_RNA,MIR3972,PADI1,PADI3,RP11-380J14.1,AC004824.1,AC004824.2,PADI4,PADI6,RCC2,RP1-20B21.4,snoU13,ACTL8,ARHGEF10L,RP11-473A10.2,RP11-174G17.2,IGSF21,IGSF21,RP11-174G17,IGSF21,RP11-422P22.1,KLHDC7A,RP1-8B22.1,RP1-8B22.2,PAX7,ALDH4A1,IFFO2,MIR1290,MIR4695,RP13-279N23.2,TAS1R2,AKR7A2,AKR7A3,AKR7L,AL137127.1,CAPZB,EMC1,MRTO4,PQLC2,RN7SL277P,RN7SL85P,RNU6-1099P,RP1-43E13.2,RP4-657E11.10,RP5-1126H10.2,UBR4,RNU4-28P,HTR6,MINOS1,MINOS1-NBL1,NBL1,RNF186,RP11-91K11.2,RP5-1056L3.1,RPS14P3,TMCO4,OTUD3,PLA2G2E,PLA2G2A,RN7SL304P,PLA2G5,PLA2G2C,PLA2G2D,PLA2G2F,RP3-340N1.2,UBXN10,UBXN10-AS1,RP3-340N1.6,LINC01141,RP4-745E8.2,RP4-749H3.2,VWA5B1,CAMK2N1,MUL1,RPS4XP4,FAM43B,AL031005.1,AL391357.1,CDA,DDOST,EIF4G3,HP1BP3,HSPE1P27,KIF17,MIR1256,PINK1,PINK1-AS,RNU7-200P,RP11-487E1.2,RP5-930J4.2,RP5-930J4.4,RP5-930J4.5,RPS15AP6,SH2D5,ECE1,RP3-329E20.2,RP5-1071N3.1,CROCCP5,HS6ST1P1,NBPF2P,NBPF3,PFN1P10,PPP1R11P1,RP11-293F5.1,RP11-293F5.8,AL359815.1,ALPL,RAP1GAP,RP11-132G19.3,RP11-63N8.3,USP48,HSPG2,LDLRAD2,RP11-26H16.1,CELA3A,CELA3B,LINC00339,RN7SL186P,RN7SL386P,RN7SL421P,RN7SL768P,RNU6-1022P,RNU6-776P,RP1-224A6.3,CDC42,CDC42-IT1,RP1-224A6.8,RP1-224A6.9,WNT4,MIR4418,RP11-415K20.1,ZBTB40,ZBTB40-IT1,EPHA8,C1QA,C1QB,C1QC,AL611946.1,EPHB2,MIR4253,MIR4684,RP1-74M1.3,RP11-69E9.1,LACTBL1,C1orf234,HTR1D,KDM1A,LUZP1,MIR3115,MIR4419A,RNU6-135P,RNU6-514P,RP1-184J9.2,RP5-979D14.1,RP5-1057J7.1,ASAP3,C1orf213,HNRNPR,RP4-654C18.1,RP5-1057J7.6,RP5-1057J7.7,TCEA3,Y_RNA,ZNF436,E2F2,ID3,RP1-150O5.3,MDS2,RP11-223J15.2,RP5-886K2.1,RPL11,CNR2,FUCA1,GALE,HMGCL,LYPLA2,MIR378F,PITHD1,PNRC2,RN7SL24P,RN7SL532P,RP11-4M23.2,RP11-4M23.3,RP11-4M23.4,RP5-886K2.3,SRSF10,TCEB3,snoU13,RP11-4M23.7,AL590683.1,IFNLR1,IL22RA1,MYOM3,RP11-10N16.2,RP11-293P20.2,RP11-293P20.4,AL590683.2,GRHL3,NIPAL3,RP11-10N16.3,STPG1,NCMAP,RCAN3,RN7SL857P,RP11-496D1.2,RP4-594I10.3,SRRM1,Y_RNA,snoU13,CLIC4,RNU6-1208P,RP11-84D1.1,RP11-84D1.2,RUNX3,MIR4425,RP4-781L3.1,RP4-799D16.1,AL031284.1,C1orf63,RHCE,RHD,RNU6-1171P,RP11-335G20.7,RP3-465N24.5,RP3-465N24.6,RP3-469D22.1,RP4-706G24.1,SDHDP6,SYF2,TMEM50A,TMEM57,snoU13,LDLRAP1,RP11-70P17.1,AL020996.1,AL033528.1,AUNIP,MAN1C1,MIR3917,MTFR1L,PAQR7,RP1-125I3.2,RP1-125I3.4,RP1-187B23.1,RP1-317E23.3,RP1-317E23.6,RP1-317E23.7,SEPN1,SNRPFP2,STMN1,Y_RNA,AL391650.1,EXTL1,PAFAH2,RNU6-110P,SCARNA17,SCARNA18,SLC30A2,TRIM63,PDIK1L,AIM1L,CATSPER4,CD52,CEP85,CNKSR1,FAM110D,RN7SL490P,RP11-231P20.2,RP11-231P20.5,RP11-569G9.7,RP11-96L14.7,SH3BGRL3,UBXN11,ZNF593,ZNF683,DHDDS,HMGN2,LIN28A,RP3-476K8.3,RP3-476K8.4,DPPA2P2,MIR1976,RN7SL679P,RPS6KA1,Y_RNA,RP11-492M19.3,RP4-785J1.1,snoU13,ARID1A,C1orf172,FAM46B,GPATCH3,GPN2,NR0B2,NUDC,OSTCP2,PIGV,RN7SL165P,RN7SL501P,RP1-50O24.6,RP11-344H11.4,RP11-344H11.5,RP5-968P14.2,SFN,TRNP1,ZDHHC18,RP11-40H20.5,SLC9A1,CD164L2,CHCHD3P3,FCN3,GPR3,MAP3K6,NPM1P39,RNU6-48P,RP1-144C9.2,RP11-40H20.4,RP11-4K3__A.3,RP11-4K3__A.5,RP4-752I6.1,SNRPEP7,SYTL1,TMEM222,WASF2,WDTC1,Y_RNA,AHDC1,CHMP1AP1,FGR,IFI6,RNU6-424P,RNU6-949P,RP1-159A19.3,RP1-159A19.4,RP11-288L9.1,RP11-288L9.4,AL109927.1,FAM76A,PPP1R8,RNU6-1245P,RP3-426I6.2,RP3-426I6.5,RP3-426I6.6,RPEP3,SCARNA1,STX12,RPA2,THEMIS2,EYA3,RN7SL559P,RP11-460I13.2,RP11-460I13.6,RP5-1053E7.2,RP5-1053E7.3,SMPDL3B,SPCS2P4,XKR8,AL353354.1,AL353354.2,ATPIF1,DNAJC8,PTAFR,RNU6-176P,RNU7-29P,RP5-1092A3.4,RP5-1092A3.5,SESN2,MED18,GMEB1,PHACTR4,PRDX3P2,RAB42,RCC1,RNU11,RNU6ATAC27P,RP1-308E4.1,RP11-442N24__B.1,SCARNA24,SNHG12,SNHG3,SNORA73B,SNORD99,TAF12,TRNAU1AP,YTHDF2,Y_RNA,snoU13,EPB41,OPRD1,RP1-212P9.2,RP1-212P9.3,RP4-604A21.1,TMEM200B,Y_RNA,AL645859.1,MECR,PTPRU,RP11-242O24.3,RP11-242O24.5,RP11-467D18.2,RP3-437I16.1,SRSF4,AL139151.1,RP11-810H18.1,AC092265.1,RP4-656G21.1,AL645944.1,RP11-179G8.1,RP11-111I12.1,RP5-893G23.1,RP3-357I16.1,RP4-591L5.1,RP4-591L5.2,LAPTM5,MATN1,MATN1-AS1,MIR4420,RN7SKP91,RP1-65J11.1,RP1-65J11.5,RP5-1125N11.1,SDC3,PUM1,RP11-201O14.1,RP11-201O14.2,SNORD103A,SNORD103B,SNORD85,RP11-490K7.1,SEPW1P,NKAIN1,FABP3,RP11-266K22.2,RP11-490K7.4,SNRNP40,ZCCHC17,AC114494.1,SERINC2,RNU6-40P,RP11-439L8.2,RP11-439L8.3,RP11-439L8.4,RP11-73M7.1,TINAGL1,COL16A1,HCRTR1,PEF1,RP11-73M7.6,RP11-73M7.9,BAI2,MIR4254,RP11-84A19.3,SPOCD1,AL136115.1,PTP4A2,RP11-84A19.2,RP11-84A19.4,RP4-534N18.2,BSDC1,CCDC28B,DCDC2B,EIF3I,FAM167B,FAM229A,GAPDHP20,HDAC1,IQCC,KHDRBS1,KPNA6,LCK,LRRC37A12P,MARCKSL1,MIR5585,MTMR9LP,RP11-277A4.4,RP11-395N6.4,RP4-622L5.2,RP4-622L5.7,RP4-811H24.9,TMEM234,TMEM39B,TSSK3,TXLNA,Y_RNA,RN7SL122P,RP1-27O5.3,ZBTB8B,FNDC5,HPCA,KIAA1522,RBBP4,RP1-27O5.3,RP11-114B7.6,S100PBP,SYNC,TMEM54,YARS,Y_RNA,ZBTB8A,ZBTB8OS,ADC,AK2,AL031602.1,FKSG48,RNF19B,RP1-117O3.2,RP4-803A2.1,RP4-803A2.2,TRIM62,A3GALT2,AL138837.1,AL513327.1,MIR3605,PHC2,RN7SKP16,RP11-415J8.3,RP11-415J8.5,RP11-415J8.7,ZNF362,CSMD2,HSPD1P14,RP4-580O19.2,TLR12P,ZSCAN20,CSMD2,HMGB4,RP5-1007G16.1,CSMD2,RNA5SP42,AC115286.1,C1orf94,CSMD2,RP4-657M3.2,MIR552,SMIM12,AL121988.1,GJA4,GJB3,GJB4,GJB5,RP1-34M23.5,SMIM12,DLGAP3,RP5-997D16.2,SMIM12,SNORD112,RP11-244H3.1,RP11-244H3.4,ZMYM6,ZMYM6NB,EFCAB14P1,RP11-248I9.2,ZMYM1,SFPQ,Y_RNA,KIAA0319L,NCDN,PSMB2,RN7SL136P,RN7SL503P,RNY5P1,RP4-728D4.2,RP4-728D4.3,RPL5P4,SNORA62,TFAP2E,ZMYM4,ZMYM4-AS1,C1orf216,CLSPN,RN7SL281P,RP11-435D7.3,ADPRHL2,AGO1,AGO3,AGO4,COL8A2,MAP7D1,RN7SL131P,RP4-665N4.4,RP4-665N4.8,RP4-789D17.4,RP4-789D17.5,TEKT2,TRAPPC3,CSF3R,EVA1B,LSM10,MRPS15,OSCP1,RNU4-27P,RP11-268J15.5,SH3D21,SNORA63,STK40,THRAP3,UBE2V2P4,FTLP18,GRIK3,RP4-614N24.1,GRIK3,MIR4255,RNU6-636P,RNA5SP43,RP5-1180C18.1,RPS29P6,DNALI1,FTH1P1,GNL2,LINC01137,MEAF6,MIR5581,RP3-423B22.5,RSPO1,SNIP1,ZC3H12A,RSPO1,ACTN4P2,AL929472.1,C1orf109,C1orf122,CDCA8,EPHA10,FHL3,INPP5B,MANEAL,MIR3659,MTF1,POU3F1,RNU6-510P,RNU6-584P,RP11-109P14.10,RP11-109P14.2,RP11-109P14.8,RP11-109P14.9,RP5-884C9.2,RP5-884C9.3,SF3A3,SNORA63,UTP11L,YRDC,Y_RNA,snoU13,RP11-214L19.1,RNU6-753P,RP11-329N22.1,RP11-334L9.1,GJA9,MYCBP,RHBDL2,RNU6-605P,RP11-781D11.1,RP5-864K19.4,RRAGC,Y_RNA,AKIRIN1,NDUFS5,BMP8A,HSPE1P8,KIAA0754,MACF1,OXCT2P1,PABPC4,PPIEL,RNA5SP44,RNU6-608P,RP11-416A14.1,RP11-420K8.1,RP11-69E11.4,RP11-69E11.8,SNORA55,BMP8B,HEYL,HPCAL4,NT5C1A,OXCT2,PPIE,RNU7-121P,RP1-118J21.24,RP1-118J21.25,RP1-144F13.3,RP1-144F13.4,MFSD2A,MYCL,RP1-118J21.5,RP3-342P20.2,TRIT1,Y_RNA,CAP1,PPT1,RP11-115D7.3,COL9A2,RLF,RNU6-1237P,RP1-228H13.1,RP1-228H13.2,RP1-39G22.4,RP1-39G22.7,SMAP2,TMCO2,ZMPSTE24,EXO5,RP1-228H13.5,RP1-63P18.2,RP11-656D10.3,RP11-656D10.5,RP11-656D10.6,ZFP69,ZFP69B,ZNF684,GTF2F2P2,KCNQ4,MIR30C1,MIR30E,NFYC,NFYC-AS1,RIMS3,RN7SL326P,RP4-739H11.3,CITED4,RP5-1066H13.4,RP11-348A7.1,UBE2V1P8,CTPS1,RP11-399E6.1,RP11-399E6.2,RP4-635E8.1,SCMH1,SLFNL1,FOXO6,RP11-399E6.4,EDN2,RNA5SP45,HIVEP3,RP11-486B10.3,RP11-486B10.4,HIVEP3,AL451006.1,HIVEP3,HIVEP3,HNRNPFP1,FOXJ3,GUCA2A,GUCA2B,RP11-223A3.1,RP11-319C21.1,CCDC30,PPCS,PPIH,RIMKLA,RNU6-536P,RP11-157D18.2,RP11-163G10.2,RP11-163G10.4,RP5-994D16.3,TMSB4XP1,YBX1,ZMYND12,C1orf50,CCDC23,CLDN19,ERMAP,LEPRE1,RP11-342M1.3,RP5-994D16.9,ZNF691,ATP6V1E1P1,RP11-342M1.6,RP11-342M1.7,RNU6-880P,SLC2A1,SLC2A1-AS1,RNU6-870P,C1orf210,CDC20,EBNA1BP2,ELOVL1,FAM183A,HYI,HYI-AS1,MED8,MPL,RNA5SP46,RP1-92O14.3,RP1-92O14.6,SZT2,SZT2-AS1,TIE1,TMEM125,WDR65,PTPRF,ARTN,ATP6V0B,B4GALT2,CCDC24,DPH2,IPO13,KDM4A,KDM4A-AS1,KLF17,KRT8P47,OOSP1P1,RN7SL479P,RNU6-1058P,RP11-184I16.3,RP11-184I16.4,RP11-570P14.1,RP11-7O11.3,RP4-675G8.2,RP4-675G8.3,RP5-1198O20.4,RP5-1198O20.5,RP5-891H21.1,RP5-891H21.5,SHMT1P1,SLC6A9,ST3GAL3,Y_RNA,AL390776.1,DMAP1,ERI3,ERI3-IT1,RNF220,RNU6-369P,MIR5584,RNF220,AL136380.1,AL359473.1,BEST4,BTBD19,C1orf228,CCNB1IP1P1,EIF2B3,HECTD3,KIF2C,MRPS17P1,OSTCP5,PLK3,PTCH2,RNA5SP47,RNF220,RNU5D-1,RNU5E-6P,RNU5F-1,RP11-269F19.2,RP5-882O7.1,RP5-882O7.4,RPS15AP11,RPS8,SNORD38A,SNORD38B,SNORD46,SNORD55,TCTEX1D4,TMEM53,UROD,ZSWIM5,AL592294.1,ZSWIM5,AKR1A1,CCDC163P,CCDC17,GPBP1L1,HMGB1P48,HPDL,IPP,MMACHC,MUTYH,NASP,PRDX1,RP11-291L19.1,RP11-767N6.2,RP11-767N6.7,RPS15AP10,TESK2,TMEM69,TOE1,snoU13,MAST2,RP11-630I5.1,MAST2,TMA16P2,LURAP1,MAST2,PIK3R3,POMGNT1,RP11-322N21.2,RP4-533D7.3,RP4-533D7.4,RP4-533D7.5,TSPAN1,LRRC41,RAD54L,UQCRH,NSUN4,RP4-603I14.3,FAAH,LINC00505,RP5-1109J22.1,RP5-1109J22.2,DMBX1,ATPAF1,EFCAB14,EFCAB14-AS1,KNCN,MKNK1,MKNK1-AS1,MOB3C,RP11-8J9.1,TEX38,CYP4B1,RP11-8J9.5,CYP4Z2P,RP11-346M5.1,CYP4A11,CYP4A22,CYP4A22-AS1,CYP4A26P,CYP4A27P,CYP4A43P,CYP4A44P,CYP4X1,CYP4Z1,LINC00853,MTND1P34,PDZK1IP1,RP11-184J23.2,CMPK1,FOXD2,FOXD2-AS1,FOXE3,RP1-18D14.7,RP11-511I2.2,STIL,TAL1,AL356458.1,RP4-666O22.3,RPL21P24,ATP6V0E1P4,AL591415.1,RP11-543D5.1,FLJ00388,RP11-543D5.2,TRABD2B,RP11-330M19.1,TRABD2B,TRABD2B,AL109659.1,CYP46A4P,RP11-193P11.3,RP4-683M8.2,SKINTL,RP5-1024N4.2,RP5-1024N4.4,SLC5A9,PPP1R8P1,RNU4-61P,RNU6-723P,RP11-329A14.1,SPATA6,RP11-329A14.2,AGBL4,AGBL4,BEND5,AGBL4,RP11-141A19.1,AGBL4,RP11-141A19.1,snoU13,AGBL4,RP11-141A19.2,AGBL4,AGBL4-IT1,AGBL4,RP5-926E3.1,AGBL4,ZNF859P,AGBL4,AL645730.1,AL645730.2,AGBL4,MTND2P29,ELAVL4,RP11-492I2.1,RP11-567C20.2,RP11-567C20.3,RP11-183G22.1,DMRTA2,FAF1,FCF1P6,HMGB1P45,RNU6-1026P,RP5-850O15.3,RP5-850O15.4,Y_RNA,FAF1,RNU6-1253P,FAF1,PHBP12,FAF1,MRPS6P2,CDKN2C,FAF1,MIR4421,C1orf185,CFL1P2,Y_RNA,AL162430.1,AL162430.2,CALR4P,EPS15,GAPDHP51,MIR761,NRD1,OSBPL9,RNF11,RNU6-1281P,RNU6-877P,RP11-191G24.1,RP11-253A20.1,RP11-275F13.1,RP11-275F13.3,RP11-296A18.3,RP11-296A18.5,RP11-296A18.6,RP4-657D16.3,RP4-657D16.6,SLC25A6P3,SNORA26,TSEN15P2,TTC39A,Y_RNA,snoU13,AL589663.1,RAB3B,RN7SL290P,RNA5SP48,RP11-91A18.1,BTF3L4,KTI12,RP11-91A18.4,TXNDC12,TXNDC12-AS1,ANAPC10P1,CC2D1B,DNAJC19P7,EEF1GP7,ORC1,PDCL3P6,PLA2G12AP1,PRPF38A,RN7SL788P,RP11-155O18.6,RP11-25O10.2,RP4-800M22.1,RP4-800M22.2,RP4-800M22.4,ZCCHC11,ZFYVE9,snoU13,GPX7,COA7,ECHDC2,FAM159A,HIGD1AP11,MIR1273F,MIR1273G,MIR5095,NDUFS5P3,PODN,RN7SL62P,RNU2-30P,RNU6-969P,RP11-159C21.4,RP11-334A14.2,RP11-334A14.5,RP11-334A14.8,RP4-631H13.2,RP4-631H13.4,RP4-631H13.5,RP4-631H13.6,SCP2,SLC1A7,TUBBP10,ZYG11A,ZYG11B,C1orf123,CPT2,LRP8,MAGOH,RP11-117D22.1,RP11-117D22.2,RP4-784A16.1,RP4-784A16.2,RP4-784A16.3,RP4-784A16.4,RP4-784A16.5,RP5-1024G6.2,RP5-1024G6.5,RP5-1024G6.7,RP5-1024G6.8,DMRTB1,SLC25A3P1,GLIS1,GLIS1,RNU7-95P,AL049745.1,DIO1,HNRNPA3P12,HSPB11,LRRC42,NDC1,RP4-654H19.2,SNORA58,YIPF1,AL161915.1,AL353898.1,AL353898.2,AL353898.3,LDLRAD1,MIR4781,RP4-758J24.4,RP4-758J24.5,TCEANC2,TMEM59,AL357673.1,CDCP2,CYB5RL,MRPL37,RP11-446E24.4,RP4-705F19.1,RP5-997D24.3,SSBP3,SSBP3-AS1,AC099796.1,ACOT11,C1orf177,DHCR24,FAM151A,HNRNPA1P63,MROH7,MROH7-TTC4,PARS2,RP11-240D10.4,RP11-67L3.2,RP11-67L3.4,RP11-67L3.5,RP5-866L20.1,RP5-866L20.2,SNORD112,TTC22,TTC4,BSND,RP11-12C17.2,TMEM61,PCSK9,USP24,GYG1P3,MIR4422,RP11-101C11.1,USP24,GOT2P1,RN7SKP291,RP4-633H17.2,RNU6-830P,RP11-466L17.1,RP11-90C4.1,PIGQP1,RP11-90C4.2,RP11-90C4.3,RP1-158P9.1,RP4-710M16.1,RP11-504A18.1,AC119674.1,RP4-710M16.2,C1orf168,PPAP2B,PRKAA2,RP11-377K22.2,RP11-377K22.3,RP11-378I13.1,RPL21P23,AL161740.1,C8A,C8B,DAB1,RP5-1103B4.3,DAB1,DAB1,RP6-102O10.1,DAB1,RPS20P5,AL137855.1,DAB1,DAB1,DAB1-AS1,DAB1,HNRNPA1P6,RP11-393I23.3,RP11-393I23.4,RPS26P15,DAB1,RP11-414C16.1,DAB1,OMA1,RN7SL713P,RP4-592A1.4,TACSTD2,RP4-592A1.2,MYSM1,AL136985.1,JUN,LINC01135,LINC01135,RP11-63G10.3,LINC01135,RP11-63G10.2,LINC01135,RP4-794H19.1,PHBP3,RP11-145M4.1,RP11-145M4.2,RP11-145M4.3,RP4-794H19.4,RP11-470E16.1,FGGY,RP11-467C18.1,FGGY,MIR4711,RP4-782L23.1,RP4-782L23.2,CYP2J2,HOOK1,C1orf87,RN7SL475P,PGBD4P8,RP11-575B7.3,RP11-776H12.1,RP11-436K8.1,RP11-776H12.1,RP11-436K8.1,NFIA,NFIA,RP4-668G5.1,AC096534.1,NFIA,RP4-802A10.1,NFIA,RP5-833A20.1,AC099791.1,RP11-430G17.1,INADL,LAMTOR5P1,MIR3116-2,RN7SL180P,RNU6-1177P,RNU6-414P,RP11-430G17.3,TM2D1,L1TD1,PIGPP2,RP5-1155K23.4,RPS15AP7,Y_RNA,KANK4,RNU6-371P,AL138847.1,ANGPTL3,DOCK7,RP11-230B22.1,RP11-293K19.1,RP5-849H19.2,USP1,ATG4C,RP4-771M4.2,RP4-771M4.3,RP11-5P4.1,RP11-5P4.2,RP11-5P4.3,RP11-335E6.2,RP11-335E6.4,AL138935.1,FOXD3,LINC00466,RNA5SP49,RP11-335E6.3,RP4-792G4.2,Y_RNA,ALG6,DLEU2L,EFCAB7,ITGB3BP,PGM1,RN7SL130P,RN7SL488P,RNU7-123P,RP4-792G4.3,ROR1,RP4-597J3.1,CFL1P3,ROR1,RNU6-809P,ROR1,ROR1,Y_RNA,ROR1,RP11-24J23.2,UBE2U,RNU7-62P,CACHD1,MIR4794,CACHD1,JAK1,RAVER2,RNU6-1176P,RP11-182I10.1,RP11-182I10.2,RP11-182I10.3,RP4-535B20.4,SLC2A3P2,MIR101-1,MIR3671,MRPS21P1,RP4-535B20.1,RP4-535B20.2,AK4,COX6CP13,DNAJC6,LEPR,LEPROT,RNU2-15P,RP4-700A9.1,RP5-1044H5.1,LEPR,RP4-630A11.3,LEPR,RP11-430H12.2,snoU13,RN7SL854P,PDE4B,PDE4B,RP11-397C12.1,PDE4B,RNU4-88P,AL139147.1,AL354978.1,INSL5,MIER1,MIR3117,RP11-342H21.2,SGIP1,SLC35D1,TCTEX1D1,WDR78,AL109843.1,C1orf141,IL23R,RNU4ATAC4P,RNU6-586P,RP4-763G1.1,SNORA31,IL12RB2,RNU6-387P,SERBP1,RNU6-1031P,RP11-393N21.1,RP4-763G1.2,HNRNPCP9,RN7SL392P,GADD45A,GNG12,GNG12-AS1,RNU7-80P,AL157407.1,ARL5AP3,DIRAS3,GNG12-AS1,RP4-609E1.2,CTBP2P8,GNG12-AS1,MIR1262,RPS7P4,WLS,COX6B1P7,RP5-1033K19.2,TCEB1P18,RPE65,DEPDC1,RP4-694A7.2,RP4-694A7.4,TXNP2,RP11-424D14.1,RP11-74K19.1,RP3-380B4.1,LRRC7,LRRC7,RP11-379C1.1,LRRC7,RN7SL538P,LRRC7,PIN1P1,LRRC7,RP11-181B18.1,ANKRD13C,HHLA3,LRRC40,LRRC7,RN7SL242P,RP11-180O5.2,RP4-677H15.4,SRSF11,CTH,RP11-42O15.3,RP11-42O15.2,CASP3P1,RP11-99H8.1,RP5-952N6.1,MIR186,PTGER3,RP3-333A15.1,RP3-333A15.2,ZRANB2,ZRANB2-AS1,ZRANB2-AS2,AL360297.1,ZRANB2-AS2,RP11-386O9.2,ZRANB2-AS2,RP11-115M14.1,ZRANB2-AS2,NEGR1,ZRANB2-AS2,NEGR1,RP11-82L20.1,NEGR1,NEGR1,RP11-175G14.2,NEGR1,NEGR1-IT1,GDI2P2,NEGR1,RPL31P12,RNU6-1246P,RP11-262K1.1,RP4-660H19.1,RP4-660H19.1,KRT8P21,RN7SKP19,RP4-598G3.1,RP4-788P17.1,RNA5SP50,RNU4ATAC8P,FPGT,FPGT-TNNI3K,LRRIQ3,TNNI3K,FPGT-TNNI3K,LRRC53,RP11-439H8.4,RP4-650F12.2,TNNI3K,C1orf173,RP4-612J11.1,CRYZ,RP11-17E13.2,TYW3,RP11-93N20.1,LHX8,RP11-510C10.2,RP11-510C10.3,RP11-510C10.4,RNU6-622P,SLC44A5,SLC44A5,RNU6-503P,RP11-87O11.1,SLC44A5,RP4-595K12.1,SLC44A5,RP4-595K12.2,ACADM,MSH4,RABGGTB,RP4-682C21.2,RP4-682C21.5,SNORD45A,SNORD45B,SNORD45C,AL445464.1,MSH4,ASB17,MSH4,RP11-550H2.1,RP11-550H2.2,ST6GALNAC3,ST6GALNAC3,RP11-335E14.1,ST6GALNAC3,RP5-1102E8.3,ST6GALNAC3,AC104458.1,TPI1P1,RNU6-161P,RP11-415A20.1,ST6GALNAC5,AC096951.1,PIGK,RP11-363H12.1,RP4-564M11.2,RP4-706A16.3,ST6GALNAC5,AC095030.1,AK5,RNU7-8P,RP11-375A5.1,AK5,DNAJB4,FAM73A,FUBP1,GIPC2,HSPE1P25,NEXN,NEXN-AS1,NSRP1P1,RN7SL370P,RNA5SP20,RNA5SP21,RNA5SP22,RNU6-1102P,RP11-181C21.4,RP11-386I14.2,RP11-386I14.3,RP11-386I14.4,RP4-706L14.2,USP33,ZZZ3,RNFT1P2,PTGFR,RNA5SP23,RP11-183M13.1,RP11-472F19.1,PTGFR,IFI44,IFI44L,RP4-641G12.3 -16.7929    106713  72544.6
chr1    79137895    84599602    IFI44,IFI44L,RP4-641G12.3,AC104837.1,RP4-641G12.4,ELTD1,PSAT1P3,AC093430.1,RP4-726F1.1,ADH5P2,RP11-339A11.1,RP11-339A11.2,HMGB1P18,AL606519.1,RP11-339D23.1,HNRNPA1P64,RP11-115A15.4,RP11-115A15.2,RP11-115A15.1,RP5-887A10.1,RP5-887A10.1,MTND2P30,RPL7P10,RP3-445O10.1,RN7SKP247,LPHN2,HNRNPA3P14,LPHN2,LPHN2,MED28P8,RP5-837I24.1,RP5-837I24.2,RP5-837I24.6,LPHN2,RP5-837I24.4,RP5-837I24.5,LPHN2,ST13P20,RP11-147G16.1,RP11-170N11.1,RP4-601K24.1,RP4-601K24.1,RP11-413G15.1,RP11-475O6.1,AL035706.1,RP11-475O6.1,RP4-552O12.1,RP5-836J3.1,TTLL7,TTLL7-IT1,PRKACB,RP11-486G15.1,RP11-486G15.2,RP11-82H13.2  -17.0226    3068    2088.63
chr1    84599602    84606611    PRKACB,RP11-486G15.1,RP11-486G15.2,RP11-82H13.2 -8.78833    14  9.48444
chr1    84606611    109651011   PRKACB,RP11-486G15.1,RP11-486G15.2,RP11-82H13.2,SNORA2,DNASE2B,RP11-376N17.4,SAMD13,UOX,CTBS,GNG5,RPF1,SPATA1,C1orf180,RP11-484D4.3,SSX2IP,AC104169.1,LPAR3,MCOLN2,MCOLN3,MIR4423,WDR63,SYDE2,AL590113.1,BCL10,C1orf52,RP11-131L23.1,Y_RNA,CYR61,DDAH1,RP11-131L23.1,RP11-131L23.2,RP11-290M5.2,RP11-290M5.4,SNORD81,Y_RNA,ZNHIT6,COL24A1,COL24A1,RNA5SP51,COL24A1,RP4-682E18.1,CLCA1,CLCA2,ODF2L,RP11-444C12.1,CLCA4,RP4-651E10.3,RP4-651E10.4,AL356270.1,RP4-651E10.4,CLCA3P,RP4-651E10.4,RP4-612B15.3,RP4-651E10.4,SH3GLB1,RP4-612B15.2,AL139139.1,HS2ST1,LINC01140,RP11-384B12.2,RP11-384B12.3,RP4-604K5.2,RP4-604K5.3,RP5-1052I5.2,SEP15,LMO4,RP4-544H6.2,RNA5SP52,RP5-1027O11.1,CTA-21C21.1,RN7SL583P,RP11-76N22.1,RP11-76N22.2,RPL36AP10,GTF2B,PKN2,RNU6-125P,RP11-76N22.2,TCEB1P19,CCBL2,GBP3,RBMXL1,RP11-82K18.2,Y_RNA,GBP1,GBP2,GBP4,GBP7,PTGES3P1,GBP5,RP4-620F22.2,RP4-620F22.3,RP5-908D6.1,CAPNS1P1,GBP1P1,GBP6,LRRC8B,LRRC8C,RP11-302M6.4,RP11-413E1.2,RP11-413E1.4,RP5-1007M22.2,RP5-943J3.1,snoU13,LRRC8D,RP11-302M6.4,RP11-302M6.5,RP5-943J3.2,GEMIN8P4,RN7SKP272,ZNF326,RNU6-695P,RP5-827O9.1,U3,BARHL2,RP4-665J23.1,RP4-665J23.2,RP4-665J23.4,PHKA1P1,RPL5P6,ZNF644,FEN1P1,HFM1,Y_RNA,HFM1,CDC7,RP11-47K11.2,RP11-91I11.1,HSP90B3P,RN7SL653P,TGFBR3,ACTBP12,AL451010.1,BRDT,BTBD8,C1orf146,EPHX4,GAPDHP46,GLMN,KIAA1107,LPCAT2BP,PRKAR1AP,RN7SL235P,RN7SL824P,RP4-621B10.8,RP4-775D17.1,RPAP2,SETSIP,GFI1,CCNJP2,EVI5,HMGB3P9,RNU4-59P,RP11-330C7.3,RP11-330C7.4,RP4-593M8.1,FAM69A,RPL5,SNORA51,SNORA66,SNORD21,FAM69A,RP11-386I23.1,AC093577.1,FAM69A,RN7SL692P,RNU6-970P,RN7SKP123,RNU6-210P,Y_RNA,CCDC18,DR1,MTF2,RP4-612C19.1,RP4-612C19.2,RP4-713B5.2,RP4-717I23.2,RP4-717I23.3,TMED5,Y_RNA,BCAR3,FNBP1L,RNA5SP53,RP5-1033H22.2,BCAR3,RP11-488P3.1,BCAR3,CHCHD2P5,DNTTIP2,GCLM,MIR760,MTND4P11,RP4-561L24.3,RP5-837O21.1,RP5-837O21.2,RP5-837O21.3,RP5-837O21.4,RP5-837O21.5,RP5-837O21.6,RP5-837O21.8,ABCA4,ARHGAP29,RN7SL440P,RP11-148B18.1,RP11-78O9.1,snoU13,GAPDHP29,RP11-148B18.3,RP11-148B18.4,ABCD3,F3,RP11-366L18.1,RP11-86H7.6,ALG14,CNN3,KATNBL1P2,LINC01057,MIR378G,PGBD4P7,RP11-313A24.1,RP11-465K1.2,RP11-86H7.7,RP4-639F20.1,SLC44A3,RP11-57H12.2,RP11-57H12.3,RP11-57H12.5,RWDD3,TMEM56,TMEM56-RWDD3,Y_RNA,RP4-586O15.1,RP11-14O19.1,RP11-14O19.2,RP4-617C6.1,AL356479.1,RP11-286B14.1,RP11-286B14.1,RP11-286B14.2,RP11-286B14.1,AC092812.1,RP11-147C23.1,RNU1-130P,RP5-898J17.1,RP4-736I12.1,RP5-898J17.1,UBE2WP1,EEF1A1P11,NDUFS5P2,RN7SL831P,RN7SKP270,RPL7P9,PTBP2,AL592205.1,AL592205.2,DPYD,DPYD-AS1,DPYD,DPYD-IT1,DPYD,SEC63P1,DPYD,RPL26P9,DPYD,DPYD,RP11-272L13.2,DPYD,DPYD-AS2,DPYD,RP11-272L13.3,RP11-272L13.4,MIR137HG,RP11-490G2.2,NFU1P2,RP5-1070A16.1,AL160056.1,SNX7,LPPR5,RP11-234N17.1,RP5-896L10.1,RP5-896L10.1,LPPR4,RP11-413P11.1,RP4-735N21.1,FRRS1,HMGB3P10,PALMD,RNU4-75P,Y_RNA,AGL,AL451051.1,RP4-581O6.1,BRI3P1,DBT,HIAT1,LRRC39,MIR553,RNU6-1318P,RNU6-750P,RP11-305E17.4,RP11-305E17.6,RP11-305E17.7,RP4-714D9.2,RP4-714D9.4,RP4-714D9.5,RP5-884G6.2,RTCA,SASS6,SLC35A3,TRMT13,AC104457.1,BCAS2P2,CDC14A,GPR88,RP5-837M10.1,RP5-837M10.2,RP5-837M10.4,RP11-84O12.2,RP11-84O12.3,RP11-84O12.4,VCAM1,AC093157.1,DPH5,EXTL2,HNRNPA1P68,RP11-421L21.2,RP11-421L21.3,RP4-549L20.3,SLC30A7,SCARNA16,RP5-1033H2.1,PPIAP7,RP4-575N6.2,RP4-575N6.4,RP4-575N6.5,S1PR1,snoU13,RP11-157N3.1,RNU6-965P,RP11-411H5.1,DNAJA1P5,OLFM3,RNU6-352P,RP11-556K13.1,RP11-82O2.2,RP11-202K23.1,RP5-936J12.1,COL11A1,SOD2P1,RP11-347K2.1,RP11-347K2.2,RP11-153F1.1,RP11-153F1.2,ACTG1P4,AMY2B,RN7SKP285,RNPC3,RP11-153F1.1,AMY2A,AMY1A,AMY1B,AMYP1,RP5-1108M17.5,AMY1C,RP11-97C18.1,RP11-364B6.1,RP11-364B6.2,FTLP17,RP11-414B7.1,RP11-251P6.1,SEPT2P1,RP11-90H3.1,RP11-90H3.2,RP11-24P14.1,RP5-947P14.1,RP5-947P14.2,RP11-478L17.1,RP11-110F24.1,RP11-233E12.1,RP11-233E12.2,RP11-233E12.4,PRMT6,NTNG1,AC114491.1,NTNG1,RP11-270C12.3,VAV3,AL591042.1,VAV3,VAV3,VAV3-AS1,AL390036.1,RP11-356N1.2,RP11-483I13.5,SLC25A24,NBPF4,NBPF5P,NBPF6,RP11-131J3.1,RP11-483I13.2,SLC25A24P1,SLC25A24P2,RP5-964H19.2,ST13P21,FAM102B,HENMT1,AKNAD1,C1orf194,CELSR2,CLCC1,FNDC7,GPSM2,KIAA1324,MYBPHL,PRPF38B,PSMA5,PSRC1,RANP5,RNU7-122P,RP11-20O24.1,RP11-20O24.4,RP11-293A10.3,RP11-475E11.2,RP5-1065J22.2,RP5-1065J22.4,RP5-1065J22.8,SARS,SCARNA2,SORT1,SPATA42,STXBP3,TAF13,TMEM167B,WDR47   -17.0609    26538   18028.2
chr1    109651011   121332322   AKNAD1,C1orf194,CELSR2,CLCC1,FNDC7,GPSM2,KIAA1324,MYBPHL,PRPF38B,PSMA5,PSRC1,RANP5,RNU7-122P,RP11-20O24.1,RP11-20O24.4,RP11-293A10.3,RP11-475E11.2,RP5-1065J22.2,RP5-1065J22.4,RP5-1065J22.8,SARS,SCARNA2,SORT1,SPATA42,STXBP3,TAF13,TMEM167B,WDR47,AMIGO1,ATXN7L2,CYB561D1,SYPL2,AC000032.2,AMPD2,EPS8L3,GNAI3,GNAT2,GPR61,GSTM1,GSTM2,GSTM3,GSTM4,GSTM5,MIR197,RNU6V,RP4-735C1.4,RP5-1160K1.3,RP5-1160K1.6,RP5-1160K1.8,RPL7P8,CSF1,NDUFA5P10,RP11-195M16.1,RP11-195M16.3,RP4-735C1.6,AHCYL1,ALX3,RP4-773N10.4,RP4-773N10.6,STRIP1,UBL4B,KCNC4,KCNC4-AS1,LAMTOR5,LAMTOR5-AS1,PROK1,RBM15,RP11-470L19.5,RP5-1028L10.1,RP5-1028L10.2,RP5-1074L1.1,RP5-1074L1.4,SLC16A4,SLC6A17,SNORA25,CYMP,RP11-470L19.2,KCNA10,KCNA2,AL365361.1,KCNA3,RP11-284N8.3,Y_RNA,CD53,NRBF2P3,OR11I1P,LRIF1,RP11-96K19.2,RP11-96K19.4,RP11-96K19.5,CCNT2P1,RNA5SP54,CEPT1,CHI3L2,CHIAP1,DENND2D,DRAM2,RP5-1180E21.4,RP5-1180E21.5,CHIA,CHIAP2,RP5-1125M8.2,RP5-1125M8.3,CHIAP3,HIGD1AP12,PGCP1,PIFO,ADORA3,ATP5F1,C1orf162,DDX20,FAM212B,FAM212B-AS1,KCND3,KRT18P57,LINC01160,OVGP1,RAP1A,RNU6-151P,RNU6-792P,RP11-552M11.4,RP11-552M11.8,UBE2FP3,WDR77,Y_RNA,KCND3,KCND3-IT1,KCND3,KCND3-AS1,KCND3,RP11-88H9.2,RP5-965F6.2,snoU13,RP5-965F6.2,TXNP3,snoU13,CAPZA1,CTTNBP2NL,FAM19A3,MOV10,MRPL53P1,PPM1J,RHOC,RNU7-70P,RP11-426L16.10,RP11-426L16.3,RP11-426L16.9,RP4-671G15.2,ST7L,WNT2B,snoU13,RP11-426L16.7,RP11-426L16.8,RP3-522D1.1,RP3-522D1.2,AKR7A2P1,LRIG2,RLIMP2,RP11-31F15.2,RP11-389O22.1,SLC16A1,SLC16A1-AS1,RP11-389O22.4,RP11-389O22.5,MAGI3,MAGI3,RP11-512F24.1,MAGI3,MTND5P20,AP4B1,AP4B1-AS1,BCL2L15,DCLRE1B,HIPK1,MAGI3,OLFML3,PHTF1,PTPN22,RP4-590F24.1,RP4-730K3.3,RP5-1073O3.2,RP5-1073O3.7,RSBN1,SYT6,RP4-543J13.1,RP4-591B8.3,EIF2S2P5,RP4-591B8.2,TRIM33,Y_RNA,PKMP1,AMPD1,BCAS2,CSDE1,DENND2C,NRAS,RN7SL432P,SIKE1,Y_RNA,NR1H5P,SYCP1,RP4-666F24.3,TSHB,TSPAN2,NGF,RP4-663N10.1,AL512638.1,RP4-663N10.2,CNOT7P2,RP11-710N8.3,TCEB1P20,CASQ2,RN7SL420P,SNORA42,VANGL1,HNRNPA1P43,NHLH2,RP11-12L8.1,RP11-12L8.2,RP11-159M11.2,SLC22A15,MAB21L3,RP5-1185H19.2,U3,AL136376.1,AL355794.1,ATP1A1,ATP1A1OS,CD58,IGSF3,MIR320B1,MIR548AC,NAP1L4P1,RNU6-817P,RP4-655J12.4,RP4-655J12.5,RP5-1086K13.1,Y_RNA,C1orf137,GAPDHP64,CD2,FTH1P22,NEFHP1,AL157904.1,CD101,MIR942,PTGFRN,RNA5SP55,RP11-27K13.3,RP4-753F5.1,RPS15AP9,TRIM45,TTF2,VTCN1,RP11-39H13.1,MAN1A2,RP11-188D8.1,VPS25P1,AL157902.3,AL365331.2,FAM46C,RP11-134N8.2,SNORA40,AL390877.1,GDAP2,SPAG17,WDR3,RNA5SP56,PSMC1P12,RP4-630J13.1,RP4-712E4.1,RP4-712E4.2,TBX15,HAO2,HAO2-IT1,RBMX2P3,RNU1-75P,RP11-418J17.1,RP11-418J17.3,RP5-834N19.1,RPL6P2,RPS3AP12,WARS2,WARS2-IT1,snoU13,GAPDHP23,HSD3B2,HSD3BP1,HSD3BP2,RP5-871G17.5,GAPDHP27,GAPDHP32,GAPDHP58,HSD3B1,HSD3BP3,HSD3BP4,GAPDHP33,HMGCS2,HSD3BP5,LINC00622,PHGDH,ZNF697,REG4,NBPF7,PFN1P9,ADAM30,NOTCH2,NOTCH2P1,RP11-114O18.1,RP5-1042I8.7,RNU6-465P,RP6-42F4.1,FAM72B,RP11-439A17.7,FCGR1B,HIST2H2BA,HIST2H3DP1,RP11-439A17.10,RP11-439A17.4,RP11-439A17.5,RP11-439A17.9,AL592494.5,RP11-343N15.1,RP11-343N15.2,RP11-343N15.5,SRGAP2C,EMBP1,RP11-344P13.1,RP11-344P13.3,RP11-344P13.4,RP11-344P13.6 -16.7745    16238   11022.6
chapmanb commented 8 years ago

Anastassiya; Glad that fixed the run issue. Regarding the outputs, it's a bit difficult to debug these remotely without more details. Given the previous result of an empty cns file and these outputs, it seems like maybe the sequencing failed or you have very poor coverage? My next step would be to look at QC outputs to determine if the mapped read results look good and if you have reasonable coverage across your target/analysis regions. Hope this helps.

anastazie commented 8 years ago

Hi Brad, thanks for your help. I think that low log2 is caused by the fact that it is not target capture NGS, for which CNVkit is primarily designed. I found that they have option for WGA here. I was using following configuration to specify that it is WGA, but may be it is not enough.

coverage_interval: genome

Can you please implement this WGA option for CNVkit into bcbio? Or if it is already present, what should I specify in configuration file?

Thank you for your great work, Anastassiya

anastazie commented 8 years ago

Sequencing data have indeed low coverage. These data were provided by manufacturer (who is unfortunately not willing to share his analysis pipeline).

I also compared commands recommended in CNVkit (first line) and command that was used by bcbio (second line) for target

cnvkit.py target data/access-5kb-mappable.hg19.bed --split --annotate refFlat.txt -o Targets.bed
cnvkit.py target cnvkit/ref-transcripts-transcripts_w10000-sort-noexclude-merged-annotated.bed --split -o cnvkit/raw/tx/tmpKcbya9/ref-transcripts-transcripts_w10000-sort-noexclude-merged-annotated.target.bed --avg-size 500

antitarget

cnvkit.py antitarget data/access-5kb-mappable.hg19.bed -g data/access-5kb-mappable.hg19.bed -o Background.bed
cnvkit.py antitarget -g cnvkit/ref-transcripts-transcripts_w10000-sort-noexclude-merged.bed cnvkit/raw/ref-transcripts-transcripts_w10000-sort-noexclude-merged-annotated.target.bed -o cnvkit/raw/tx/tmpwUrZEd/ref-transcripts-transcripts_w10000-sort-noexclude-merged-annotated.antitarget.bed

I noticed following warning in bcbio log:

WARNING: most bins have no or very low coverage; check that the right BED file was used
chapmanb commented 8 years ago

Anastassiya; I agree that CNVkit is probably not the right approach for calling low coverage whole genome data. We haven't done much with low depth data and focused more on calling with 30x+ depth. We do handle whole genome data with CNVkit, but have only run it at that higher depth. I know that some CNV callers will let you identify large scale (whole chromosome or chromosome arm losses) with low pass data, but don't have any integrated in bcbio currently and I don't have any practical experience to know which work well. The only caller that might work in bcbio currently is Battenberg (https://github.com/cancerit/cgpBattenberg) which you could try with:

svcaller: [battenberg]

Sorry to not have more experience with this type of data and hope this helps.

anastazie commented 7 years ago

Dear Brad, thank you for your suggestion. However, I couldn't use it, because it requires pair samples (tumor/normal). I ended using bcbio to generate bam files and then used Bioconductor package QDNAseq, which is suitable for low-coverage data.

chapmanb commented 7 years ago

Thanks for following up with the approach you used and glad to hear you got the analysis finished. We'd be happy to merge integration with QDNAseq inside bcbio if you end up working in that direction. Thanks again.

etal commented 7 years ago

CNVkit should work to some degree with low-coverage WGS if the bin sizes are large enough, i.e. at least ~20,000 bases per bin. Is there a filter in the current (v0.8) implementation that's interfering with this?