ex-291 (cgates): Increase rounding precision from 2 to 4 digits; fixe…

…d py3 anomalies and adjusted metaheader
umich-brcf-bioinf · Sep 4, 2015 · 997788b · 997788b
1 parent dd6a20e
commit 997788b
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Showing 30 changed files with 57 additions and 43 deletions.
diff --git a/jacquard/variant_caller_transforms/mutect.py b/jacquard/variant_caller_transforms/mutect.py
@@ -41,7 +41,7 @@ def __init__(self):
               self).__init__(MUTECT_ABBREVIATION,
                              common_tags.ALLELE_FREQ_TAG,
                              ('Jacquard allele frequency for MuTect: '
-                              'Decimal allele frequency rounded to 2 digits '
+                              'Decimal allele frequency rounded to 4 digits '
                               '(based on FA)'))
 
     def add_tag_values(self, vcf_record):

diff --git a/jacquard/variant_caller_transforms/strelka.py b/jacquard/variant_caller_transforms/strelka.py
@@ -93,7 +93,7 @@ def __init__(self):
               self).__init__(STRELKA_ABBREVIATION,
                              common_tags.ALLELE_FREQ_TAG,
                              ('Jacquard allele frequency for Strelka: Decimal '
-                              'allele frequency rounded to 2 digits (based on '
+                              'allele frequency rounded to 4 digits (based on '
                               'alt_depth/total_depth. Uses (TIR tier 2)/DP2 if '
                               'available, otherwise uses (ACGT tier2 depth) / '
                               'DP2)'))

diff --git a/jacquard/variant_caller_transforms/varscan.py b/jacquard/variant_caller_transforms/varscan.py
@@ -61,7 +61,7 @@ class _AlleleFreqTag(common_tags.AbstractJacquardTag):
     def _standardize_af(cls, value):
         new_values = []
         for val in value:
-            new_val = str(float(val.strip("%")) / 100)
+            new_val = str(round(float(val.strip("%")) / 100, 6))
             new_values.append(utils.round_digits(new_val))
         return ",".join(new_values)
 
@@ -70,7 +70,7 @@ def __init__(self):
               self).__init__(VARSCAN_ABBREVIATION,
                              common_tags.ALLELE_FREQ_TAG,
                              ('Jacquard allele frequency for VarScan: Decimal '
-                              'allele frequency rounded to 2 digits (based on '
+                              'allele frequency rounded to 4 digits (based on '
                               'FREQ)'))
 
     def add_tag_values(self, vcf_record):

diff --git a/test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf b/test/functional_tests/01_translate/benchmark/tiny.mutect.translatedTags.vcf
@@ -111,7 +111,7 @@
 ##FORMAT=<ID=FA,Number=A,Type=Float,Description="Allele fraction of the alternate allele with regard to reference">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 4 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_MT_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Integer,Description="Jacquard depth for MuTect (based on DP)">

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
@@ -58,7 +58,7 @@
 ##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1">
 ##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_SK_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)">

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
@@ -52,7 +52,7 @@
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1 (used+filtered)">
 ##FORMAT=<ID=FDP,Number=1,Type=Integer,Description="Number of basecalls filtered from original read depth for tier1">
 ##FORMAT=<ID=GU,Number=2,Type=Integer,Description="Number of 'G' alleles used in tiers 1,2">
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_SK_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,Description="Jacquard depth for Strelka (uses DP2 if available, otherwise uses ACGT tier2 depth)">

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
@@ -20,7 +20,7 @@
 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_VS_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,Description="Jacquard depth for VarScan (based on DP)">

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
@@ -20,7 +20,7 @@
 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_CALLER_PASSED,Number=1,Type=Integer,Description="1 = variant FILTER is PASS in original VCF">
 ##FORMAT=<ID=JQ_VS_CALLER_REPORTED,Number=1,Type=Integer,Description="1 = variant present in original VCF">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,Description="Jacquard depth for VarScan (based on DP)">

diff --git a/test/functional_tests/02_merge/benchmark/merged.vcf b/test/functional_tests/02_merge/benchmark/merged.vcf
@@ -7,13 +7,13 @@
 ##contig=<ID=chr3,length=198022430>
 ##contig=<ID=chr13,length=115169878>
 ##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 4 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Integer,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)">
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,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)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tiny|NORMAL	tiny|TUMOR

diff --git a/test/functional_tests/02_merge/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/02_merge/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf
@@ -112,7 +112,7 @@
 ##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 4 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Integer,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

diff --git a/test/functional_tests/02_merge/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/02_merge/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf
@@ -79,7 +79,7 @@
 ##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
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
 ##FILTER=<ID=JQ_EXCLUDE,Description="This variant record is problematic and will be excluded from downstream Jacquard processing.">

diff --git a/test/functional_tests/02_merge/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf b/test/functional_tests/02_merge/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf
@@ -20,7 +20,7 @@
 ##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,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

diff --git a/test/functional_tests/02_merge_unsorted/benchmark/merged.vcf b/test/functional_tests/02_merge_unsorted/benchmark/merged.vcf
@@ -7,13 +7,13 @@
 ##contig=<ID=chr3,length=198022430>
 ##contig=<ID=chr13,length=115169878>
 ##INFO=<ID=JQ_MULT_ALT_LOCUS,Number=0,Type=Flag,Description="More than one alt allele was seen at this locus.">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 4 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Integer,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)">
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
-##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,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)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tiny|NORMAL	tiny|TUMOR

diff --git a/...unctional_tests/02_merge_unsorted/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf b/...unctional_tests/02_merge_unsorted/input/tiny.mutect.normalized.jacquardTags.HCsomatic.vcf
@@ -112,7 +112,7 @@
 ##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for MuTect: Decimal allele frequency rounded to 4 digits (based on FA)">
 ##FORMAT=<ID=JQ_MT_DP,Number=1,Type=Integer,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

diff --git a/...nctional_tests/02_merge_unsorted/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf b/...nctional_tests/02_merge_unsorted/input/tiny.strelka.normalized.jacquardTags.HCsomatic.vcf
@@ -79,7 +79,7 @@
 ##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
-##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 (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses (TIR tier 2)/DP2 if available, otherwise uses (ACGT tier2 depth) / DP2)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
 ##FILTER=<ID=JQ_EXCLUDE,Description="This variant record is problematic and will be excluded from downstream Jacquard processing.">

diff --git a/...nctional_tests/02_merge_unsorted/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf b/...nctional_tests/02_merge_unsorted/input/tiny.varscan.normalized.jacquardTags.HCsomatic.vcf
@@ -20,7 +20,7 @@
 ##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_AF,Number=A,Type=Float,Description="Jacquard allele frequency for VarScan: Decimal allele frequency rounded to 4 digits (based on FREQ)">
 ##FORMAT=<ID=JQ_VS_DP,Number=1,Type=Integer,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

diff --git a/test/functional_tests/03_summarize/benchmark/summarized.vcf b/test/functional_tests/03_summarize/benchmark/summarized.vcf
@@ -9,7 +9,7 @@
 ##jacquard=<timestamp="2015-05-19 14:34:18",command="<module 'jacquard.summarize' from 'C:\Users\dkriti\workspace\Jacquard\jacquard\summarize.pyc'>",cwd="c:\Users\dkriti\workspace">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_PASSED_COUNT,Number=1,Type=Integer,Description="Count of samples where a variant caller passed the filter in any of the Jacquard tagged VCFs">
 ##INFO=<ID=JQ_SUMMARY_SAMPLES_REPORTED_COUNT,Number=1,Type=Integer,Description="Count of samples where this variant appeared in any of the Jacquard tagged VCFs (regardless of quality/filtering)">
-##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)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
 ##FORMAT=<ID=JQ_SUMMARY_AF_AVERAGE,Number=1,Type=Float,Description="Average allele frequency across recognized variant callers that reported frequency for this position [average(JQ_*_AF)].">

diff --git a/test/functional_tests/03_summarize/input/tiny_strelka.merged.vcf b/test/functional_tests/03_summarize/input/tiny_strelka.merged.vcf
@@ -1,4 +1,4 @@
-##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)">
+##FORMAT=<ID=JQ_SK_AF,Number=A,Type=Float,Description="Jacquard allele frequency for Strelka: Decimal allele frequency rounded to 4 digits (based on alt_depth/total_depth. Uses TAR if available, otherwise uses uses DP2 if available, otherwise uses ACGT tier2 depth)">
 ##FORMAT=<ID=JQ_SK_DP,Number=1,Type=Integer,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)">
 ##fileformat=VCFv4.2