EX-83 (cgates): Release version 0.31

umich-brcf-bioinf · Mar 19, 2015 · e1b5278 · e1b5278
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diff --git a/AUTHORS → AUTHORS.md b/AUTHORS → AUTHORS.md
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,14 @@
 Changelog
 ================
 
-## 0.3 (3/2014)
+## 0.31 (3/17/2015)
+ * Downgraded VCF format from 4.2 to 4.1
+ * Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag
+ * Simplified summary tags; removed dependency on numpy
+ * Adjusted VarScan translation to accept a file pattern to identify high-confidence files 
+
+
+## 0.3 (3/9/2015)
  * Replaced [normalize], [tag] commands with [translate]; relaxed constraints on incoming data.
  * Renamed [consensus] to [summarize]
  * More consistent behavior in [expand]

diff --git a/TODO.md b/TODO.md
@@ -8,6 +8,7 @@ TODO
 * Extend [expand] to parse SnpEff/Annovar annotated results
 * Extend [expand] to generate formatted results
 * Improve command validation (check source tags, check "shape" of inputs)
+* Enable 4.2 VCF support
 * Add support for new somatic callers
 * Add support for Germline workflows
 * Add support for Python 3

diff --git a/jacquard/__init__.py b/jacquard/__init__.py
@@ -1 +1 @@
-__version__ = 0.3
+__version__ = 0.31
diff --git a/jacquard/filter_hc_somatic.py b/jacquard/filter_hc_somatic.py
@@ -57,7 +57,7 @@ def _find_somatic_positions(in_files):
                     total_number_of_files)
         somatic = 0
         vcf_reader = vcf.VcfReader(vcf.FileReader(input_file))
-        #TODO: (jebene) - this is old. have this use claim() instead of get_caller()
+        #TODO: (jebene) - this is old. have this use claim() instead
         caller = variant_caller_factory.get_caller(vcf_reader.metaheaders,
                                                    vcf_reader.column_header,
                                                    vcf_reader.file_name)

diff --git a/jacquard/variant_callers/common_tags.py b/jacquard/variant_callers/common_tags.py
@@ -43,7 +43,7 @@ def __init__(self, tag_name):
                            'Number=1,Type=Integer,'
                            'Description="1 = variant FILTER is PASS in '
                            'original VCF">').format(self.tag_name,
-                                                   CALLER_PASSED_TAG)
+                                                    CALLER_PASSED_TAG)
 
     def add_tag_values(self, vcf_record):
         sample_values = {}

diff --git a/jacquard/variant_callers/summarize_caller.py b/jacquard/variant_callers/summarize_caller.py
@@ -9,7 +9,6 @@
 import jacquard.variant_callers.common_tags as common_tags
 import re
 
-#TODO: (cgates): Numpy is not necessary and frankly not pulling its weight.
 JQ_SUMMARY_TAG = "JQ_SUMMARY_"
 JQ_REPORTED = "CALLERS_REPORTED_COUNT"
 JQ_REPORTED_LIST = "CALLERS_REPORTED_LIST"
@@ -255,7 +254,7 @@ def add_tag_values(record):
                                               sample,
                                               _AlleleFreqRangeTag._PATTERN)
 
-            aggregated_values= "."
+            aggregated_values = "."
             if tag_values:
                 aggregated_values = _aggregate_numeric_values(tag_values,
                                                               _range)
@@ -297,7 +296,7 @@ def add_tag_values(record):
                                               sample,
                                               _AlleleFreqAverageTag._PATTERN)
 
-            aggregated_values= "."
+            aggregated_values = "."
             if tag_values:
                 aggregated_values = _aggregate_numeric_values(tag_values,
                                                               _average)
@@ -339,7 +338,7 @@ def add_tag_values(record):
                                               sample,
                                               _DepthRangeTag._PATTERN)
 
-            aggregated_values= "."
+            aggregated_values = "."
             if tag_values:
                 aggregated_values = _aggregate_numeric_values(tag_values,
                                                               _range)
@@ -381,7 +380,7 @@ def add_tag_values(record):
                                               sample,
                                               _DepthAverageTag._PATTERN)
 
-            aggregated_values= "."
+            aggregated_values = "."
             if tag_values:
                 aggregated_values = _aggregate_numeric_values(tag_values,
                                                               _average)
@@ -423,7 +422,7 @@ def add_tag_values(record):
             tag_values = _get_non_null_values(record,
                                               sample,
                                               _SomaticTag._PATTERN)
-            aggregated_values= "."
+            aggregated_values = "."
             if tag_values:
                 aggregated_values = _aggregate_numeric_values(tag_values,
                                                               _count)

diff --git a/jacquard/variant_callers/varscan.py b/jacquard/variant_callers/varscan.py
@@ -349,8 +349,8 @@ def claim(self, file_readers):
         """
 
         (prefix_vcf_readers,
-            filter_files,
-            unclaimed_set) = self._find_varscan_files(file_readers)
+         filter_files,
+         unclaimed_set) = self._find_varscan_files(file_readers)
         tuples = self._pair_files(prefix_vcf_readers, filter_files)
         self._validate_file_pairs(tuples)
         vcf_readers = self._create_vcf_readers(tuples)

diff --git a/setup.py b/setup.py
@@ -23,8 +23,8 @@ def readme():
                    'Programming Language :: Python :: 2.7',
                    'Topic :: Scientific/Engineering :: Bio-Informatics'],
       keywords='VCF bioinformatic exome-seq DNA-seq variant-call-format',
-      install_requires=['natsort', 'numpy'],
+      install_requires=['natsort'],
       entry_points={'console_scripts': ['jacquard=jacquard.jacquard:main']},
       test_suite='nose.collector',
-      tests_require=['nose', 'testfixtures'],
+      tests_require=['nose', 'testfixtures', 'numpy'],
       zip_safe=False)
diff --git a/test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf
@@ -114,7 +114,7 @@
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Float,Description="Jacquard depth for MuTect (based on DP)">
 ##FORMAT=<ID=JQ_MT_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for MuTect: 0=non-somatic,1=somatic (based on SS FORMAT tag)">
 ##jacquard.translate.caller=MuTect
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=translate C:\Users\jebene\git\Jacquard\test\functional_tests\01_translate\input C:\Users\jebene\Desktop\translate_test --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

diff --git a/test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.strelka.indels.translatedTags.vcf
@@ -63,7 +63,7 @@
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Float,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)">
 ##FORMAT=<ID=JQ_SK_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for Strelka: 0=non-somatic,1=somatic (based on PASS in FILTER column)">
 ##jacquard.translate.caller=Strelka
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=translate C:\Users\jebene\git\Jacquard\test\functional_tests\01_translate\input C:\Users\jebene\Desktop\translate_test --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

diff --git a/test/functional_tests/01_translate/benchmark/tiny.strelka.snvs.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.strelka.snvs.translatedTags.vcf
@@ -56,7 +56,7 @@
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Float,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)">
 ##FORMAT=<ID=JQ_SK_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for Strelka: 0=non-somatic,1=somatic (based on PASS in FILTER column)">
 ##jacquard.translate.caller=Strelka
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=translate C:\Users\jebene\git\Jacquard\test\functional_tests\01_translate\input C:\Users\jebene\Desktop\translate_test --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

diff --git a/test/functional_tests/01_translate/benchmark/tiny.varscan.indel.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.varscan.indel.translatedTags.vcf
@@ -22,7 +22,7 @@
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Float,Description="Jacquard depth for VarScan (based on DP)">
 ##FORMAT=<ID=JQ_VS_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for VarScan: 0=non-somatic,1=somatic (based on SOMATIC info tag and if sample is TUMOR)">
 ##jacquard.translate.caller=VarScan
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=translate C:\Users\jebene\git\Jacquard\test\functional_tests\01_translate\input C:\Users\jebene\Desktop\translate_test --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

diff --git a/test/functional_tests/01_translate/benchmark/tiny.varscan.snp.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.varscan.snp.translatedTags.vcf
@@ -22,7 +22,7 @@
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Float,Description="Jacquard depth for VarScan (based on DP)">
 ##FORMAT=<ID=JQ_VS_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for VarScan: 0=non-somatic,1=somatic (based on SOMATIC info tag and if sample is TUMOR)">
 ##jacquard.translate.caller=VarScan
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=translate C:\Users\jebene\git\Jacquard\test\functional_tests\01_translate\input C:\Users\jebene\Desktop\translate_test --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FILTER=<ID=JQ_EXCLUDE_MALFORMED_REF,Description="The format of the reference value for this variant record does not comply with VCF standard.">

diff --git a/test/functional_tests/02_tag/benchmark/tiny_strelka.normalized.jacquardTags.vcf b/test/functional_tests/02_tag/benchmark/tiny_strelka.normalized.jacquardTags.vcf
@@ -75,7 +75,7 @@
 ##source=strelka
 ##source_version=2.0.15
 ##startTime=Wed Jul  9 13:37:22 2014
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag C:\Users\jebene\Desktop\tests\tag_input C:\Users\jebene\Desktop\tests\tag_output --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##jacquard.tag.caller=Strelka

diff --git a/...l_tests/03_filter_hc_somatic/benchmark/tiny_strelka.normalized.jacquardTags.HCsomatic.vcf b/...l_tests/03_filter_hc_somatic/benchmark/tiny_strelka.normalized.jacquardTags.HCsomatic.vcf
@@ -75,15 +75,15 @@
 ##source=strelka
 ##source_version=2.0.15
 ##startTime=Wed Jul  9 13:37:22 2014
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag C:\Users\jebene\git\Jacquard\test\functional_tests\02_tag\input C:\Users\jebene\git\Jacquard\test\functional_tests\02_tag\output
 ##jacquard.cwd=C:\Users\jebene\git
 ##jacquard.tag.caller=Strelka
 ##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 2 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)",Source="Jacquard",Version=0.3>
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Float,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)",Source="Jacquard",Version=0.3>
 ##FORMAT=<ID=JQ_SK_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for Strelka: 0=non-somatic,1=somatic (based on PASS in FILTER column)",Source="Jacquard",Version=0.3>
 ##jacquard.filterHCSomatic.excluded_variants=35
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=filter_hc_somatic C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\03_filter_hc_somatic\input C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\03_filter_hc_somatic\benchmark
 ##jacquard.cwd=C:\Users\kmeng
 ##jacquard.filterHCSomatic.total_highConfidence_somatic_positions=10

diff --git a/test/functional_tests/03_filter_hc_somatic/input/tiny_strelka.normalized.jacquardTags.vcf b/test/functional_tests/03_filter_hc_somatic/input/tiny_strelka.normalized.jacquardTags.vcf
@@ -75,7 +75,7 @@
 ##source=strelka
 ##source_version=2.0.15
 ##startTime=Wed Jul  9 13:37:22 2014
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag C:\Users\jebene\git\Jacquard\test\functional_tests\02_tag\input C:\Users\jebene\git\Jacquard\test\functional_tests\02_tag\output
 ##jacquard.cwd=C:\Users\jebene\git
 ##jacquard.tag.caller=Strelka

diff --git a/test/functional_tests/04_merge/benchmark/merged.vcf b/test/functional_tests/04_merge/benchmark/merged.vcf
@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.1
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=merge2 C:\\Users\\jebene\\git\\Jacquard\\test\\functional_tests\\04_merge2\\input c:\\users\\jebene\\appdata\\local\\temp\\tmpsxyixy\\merged.vcf --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.merge.sample=<Column=1,Name=tiny|NORMAL,Source=tiny.mutect.normalized.jacquardTags.HCsomatic.vcf|tiny.strelka.normalized.jacquardTags.HCsomatic.vcf|tiny.varscan.normalized.jacquardTags.HCsomatic.vcf>

diff --git a/test/functional_tests/04_merge/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/04_merge/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf
@@ -108,15 +108,15 @@
 ##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
 ##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
 ##reference=file:ucsc.hg19.fasta
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag c:\\users\\jebene\\appdata\\local\\temp\\tmptivahf\\normalize c:\\users\\jebene\\appdata\\local\\temp\\tmptivahf\\tag --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.tag.caller=MuTect
 ##FORMAT=<ID=JQ_MT_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 2 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Float,Description="Jacquard depth for MuTect (based on DP)">
 ##FORMAT=<ID=JQ_MT_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for MuTect: 0=non-somatic,1=somatic (based on SS FORMAT tag)">
 ##jacquard.filterHCSomatic.excluded_variants=37
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=filter_hc_somatic c:\\users\\jebene\\appdata\\local\\temp\\tmptivahf\\tag c:\\users\\jebene\\appdata\\local\\temp\\tmptivahf\\filter_hc_somatic --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.filterHCSomatic.total_highConfidence_somatic_positions=12

diff --git a/test/functional_tests/04_merge/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/04_merge/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf
@@ -75,7 +75,7 @@
 ##source=strelka
 ##source_version=2.0.15
 ##startTime=Wed Jul  9 13:37:22 2014
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag c:\\users\\jebene\\appdata\\local\\temp\\tmpfyxdri\\normalize c:\\users\\jebene\\appdata\\local\\temp\\tmpfyxdri\\tag --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.tag.caller=Strelka
@@ -85,7 +85,7 @@
 ##FILTER=<ID=JQ_EXCLUDE,Description="This variant record is problematic and will be excluded from downstream Jacquard processing.">
 ##FILTER=<ID=JQ_MISSING_ALT,Description="The alternate allele is missing for this variant record.">
 ##jacquard.filterHCSomatic.excluded_variants=33
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=filter_hc_somatic c:\\users\\jebene\\appdata\\local\\temp\\tmpfyxdri\\tag c:\\users\\jebene\\appdata\\local\\temp\\tmpfyxdri\\filter_hc_somatic --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.filterHCSomatic.total_highConfidence_somatic_positions=12

diff --git a/test/functional_tests/04_merge/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/04_merge/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf
@@ -16,15 +16,15 @@
 ##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
 ##fileformat=VCFv4.1
 ##source=VarScan2
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=tag c:\\users\\jebene\\appdata\\local\\temp\\tmpfuwrpl\\normalize c:\\users\\jebene\\appdata\\local\\temp\\tmpfuwrpl\\tag --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.tag.caller=VarScan
 ##FORMAT=<ID=JQ_VS_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 2 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Float,Description="Jacquard depth for VarScan (based on DP)">
 ##FORMAT=<ID=JQ_VS_HC_SOM,Number=1,Type=Integer,Description="Jacquard somatic status for VarScan: 0=non-somatic,1=somatic (based on SOMATIC info tag and if sample is TUMOR)">
 ##jacquard.filterHCSomatic.excluded_variants=43
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=filter_hc_somatic c:\\users\\jebene\\appdata\\local\\temp\\tmpfuwrpl\\tag c:\\users\\jebene\\appdata\\local\\temp\\tmpfuwrpl\\filter_hc_somatic --force
 ##jacquard.cwd=C:\\Users\\jebene\\git
 ##jacquard.filterHCSomatic.total_highConfidence_somatic_positions=12

diff --git a/test/functional_tests/05_summarize/benchmark/summarized.vcf b/test/functional_tests/05_summarize/benchmark/summarized.vcf
@@ -1,4 +1,4 @@
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=summarize C:\Users\jebene\git\Jacquard\test\functional_tests\05_summarize\input\tiny_strelka.merged.vcf C:\Users\jebene\Desktop\summarized\summarized.vcf --force
 ##jacquard.cwd=C:\Users\jebene\git
 ##FORMAT=<ID=JQ_SUMMARY_CALLERS_REPORTED_COUNT,Number=1,Type=Integer,Description="Count of variant callers which listed this variant in the Jacquard tagged VCF">
@@ -12,7 +12,7 @@
 ##FORMAT=<ID=JQ_SUMMARY_DP_AVERAGE,Number=1,Type=Float,Description="Average allele frequency across recognized variant callers that reported frequency for this position; rounded to integer [round(average(JQ_*_DP))].">
 ##FORMAT=<ID=JQ_SUMMARY_DP_RANGE,Number=1,Type=Float,Description="Max(depth) - min (depth) across recognized callers.">
 ##FORMAT=<ID=JQ_SUMMARY_SOM_COUNT,Number=1,Type=Integer,Description="Count of recognized variant callers that reported confident somatic call for this sample-position.">
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=merge C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\04_merge\input C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\04_merge\output\tiny_strelka.merged.vcf
 ##jacquard.cwd=C:\Users\kmeng
 ##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 2 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)">

diff --git a/test/functional_tests/05_summarize/input/tiny_strelka.merged.vcf b/test/functional_tests/05_summarize/input/tiny_strelka.merged.vcf
@@ -1,4 +1,4 @@
-##jacquard.version=0.3
+##jacquard.version=X
 ##jacquard.command=merge C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\04_merge\input C:\Users\kmeng\ExomeSeqPipeline\test\functional_tests\04_merge\output\tiny_strelka.merged.vcf
 ##jacquard.cwd=C:\Users\kmeng
 ##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 2 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)">

diff --git a/test/functional_tests/06_expand/input/summarized.vcf b/test/functional_tests/06_expand/input/summarized.vcf
@@ -217,7 +217,7 @@
 ##jacquard.merge.file2=tiny_strelka.normalized.jacquardTags.HCsomatic.splitMultAlts.vcf(['NORMAL', 'TUMOR'])
 ##jacquard.merge.sample_column1=Strelka|tiny_strelka|NORMAL(tiny_strelka.normalized.jacquardTags.HCsomatic.splitMultAlts.vcf)
 ##jacquard.merge.sample_column2=Strelka|tiny_strelka|TUMOR(tiny_strelka.normalized.jacquardTags.HCsomatic.splitMultAlts.vcf)
-##jacquard.version=0.3
+##jacquard.version=X
 ##samtoolsVersion=0.1.17 (r973:277)
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tiny_strelka|NORMAL	tiny_strelka|TUMOR
 chr1	1147545	.	A	G	.	.	POPULATION_SNPFreq=Novel_locus;POPULATION_AF_CATEGORY=Novel_locus;POPULATION_AF=.;POPULATION_AF_SOURCE=.;NUCMATCH=0;in_.;SNP;VARTYPE=SNP;dbNSFP_rollup_tolerated=0;dbNSFP_rollup_damaging=0;dbNSFP_rollup_total=0;FS=GTGTGCTTCCCAGCCAAGGTGCAGCTGTTGGGGAACAGGAGGTGTTGCTC[A/G]GGCCAGAAACCCCCTGGGACCCGGGAGATGCGGTGGGGATAACAGGGTCC;SNPEFF_TOP_EFF=.;SNPEFF_TOP_EFF_FOR_GENES=.;SNPEFF_TOP_EFFECT_GENE_REGION=.;SNPEFF_TOP_EFFECT_IMPACT=.;SNPEFF_TOP_EFFECT_IMPACT_RANK=.;SNPEFF_ALL_GENE_SYMBOLS=TNFRSF4;SNPEFF_TOP_EFFECT_GENE_ID=.;SNPEFF_TOP_EFFECT_GENE_SYMBOL=.;SNPEFF_TOP_EFFECT_TRANSCRIPT_BIOTYPE=.;SNPEFF_TOP_EFFECT_AA_LENGTH=.;SNPEFF_TOP_EFFECT_TRANSCRIPT_ID=.;SNPEFF_TOP_EFFECT_AA_CHANGE=.;SNPEFF_TOP_EFFECT_EFFECT=.;EFF=sequence_feature[glycosylation_site:N-linked__GlcNAc..._](MODERATE|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|5|1),sequence_feature[glycosylation_site:N-linked__GlcNAc..._](MODERATE|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|4|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|5|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|2|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|3|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|1|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|4|1),sequence_feature[topological_domain:Extracellular](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|6|1),sequence_feature[repeat:TNFR-Cys_4](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|5|1),sequence_feature[repeat:TNFR-Cys_4](LOW|||c.438A>G|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|4|1),intron_variant(MODIFIER|||c.438-27T>C|277|ENSG00000186827|protein_coding|CODING|ENST00000379236|4|1),intron_variant(MODIFIER|||n.274-27T>C||ENSG00000186827|processed_transcript|CODING|ENST00000453580|3|1),intron_variant(MODIFIER|||n.1018-27T>C||ENSG00000186827|retained_intron|CODING|ENST00000497869|3|1);SNPEFF_WARNING_ERROR=.	JQ_SK_AF:JQ_SK_DP:JQ_SK_HC_SOM:JQ_CONS_AF:JQ_CONS_SOM_SUM:JQ_CONS_DP:JQ_CONS_AF_RANGE:JQ_CONS_DP_RANGE:JQ_CONS_AF_RANGE_ZSCORE:JQ_CONS_DP_RANGE_ZSCORE	0.0:27:0:0.0:0:27.0:0.0:0.0:0.0:0.0	0.31:35:1:0.31:1:35.0:0.0:0.0:0.0:0.0