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Update VAF cutoff default to 0.25
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@susannasiebert
susannasiebert committed Oct 3, 2018
1 parent a66b14d commit 6938c32
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Showing 7 changed files with 55 additions and 14 deletions.
3 changes: 3 additions & 0 deletions docs/index.rst
View file
Expand Up @@ -66,6 +66,9 @@ This version adds a host of new features to pVACtools:
can be run listing ``MHCflurry``, ``MHCnuggetsI`` (for MHC Class I alleles),
and/or ``MHCnuggetsII`` (for MHC Class II alleles) as the prediction
algorithms.
- The default ``--tdna-vaf`` and ``--trna-vaf`` cutoff values have been
updated from 0.4 to 0.25. This is the minimum VAF threshold that an epitope
candidate must meet in order to pass the coverage filter.
- We now offer a graphical user interface, :ref:`pvacviz`, to run pVACseq instead of using the
command line. pVACviz, can also be used to plot and filter your pVACseq
results.
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8 changes: 4 additions & 4 deletions lib/run_argument_parser.py
View file
Expand Up @@ -185,14 +185,14 @@ def __init__(self):
self.parser.add_argument(
'--tdna-vaf', type=int,
help="Tumor DNA VAF Cutoff. Sites above this cutoff will be considered. " +
"Default: 0.4",
default=0.4
"Default: 0.25",
default=0.25
)
self.parser.add_argument(
'--trna-vaf', type=int,
help="Tumor RNA VAF Cutoff. Sites above this cutoff will be considered. " +
"Default: 0.4",
default=0.4
"Default: 0.25",
default=0.25
)
self.parser.add_argument(
'--expn-val', type=int,
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4 changes: 2 additions & 2 deletions tests/test_data/api/sample_basic_run/config.json
View file
Expand Up @@ -27,11 +27,11 @@
"trna_cov": 10,
"keep_tmp_files": false,
"normal_vaf": 0.02,
"trna_vaf": 0.40,
"trna_vaf": 0.25,
"prediction_algorithms": [
"NetMHC"
],
"iedb_install_dir": "",
"tdna_vaf": 0.40,
"tdna_vaf": 0.25,
"tdna_cov": 10
}
38 changes: 38 additions & 0 deletions tests/test_data/coverage_filter/Test.filtered.coverage.tsv
View file
@@ -1,4 +1,42 @@
Chromosome Start Stop Reference Variant Transcript Ensembl Gene ID Variant Type Mutation Protein Position Gene Name HGVSc HGVSp HLA Allele Peptide Length Sub-peptide Position Mutation Position MT Epitope Seq WT Epitope Seq Best MT Score Method Best MT Score Corresponding WT Score Corresponding Fold Change Tumor DNA Depth Tumor DNA VAF Tumor RNA Depth Tumor RNA VAF Normal Depth Normal VAF Gene Expression Transcript Expression Median MT Score Median WT Score Median Fold Change NetMHC WT Score NetMHC MT Score PickPocket WT Score PickPocket MT Score
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 7 5 KFNPQTDYL KFNPETDYL PickPocket 1262.76 1318.61 1.044 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 1262.76 1318.61 1.044 NA NA 1318.61 1262.76
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 8 4 FNPQTDYLT FNPETDYLT PickPocket 2551.25 2416.9 0.947 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 16712.305 17461.505 1.045 32506.11 30873.36 2416.9 2551.25
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 8 4 FNPQTDYLTG FNPETDYLTG PickPocket 4676.23 4478.16 0.958 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 23300.735 23574.685 1.012 42671.21 41925.24 4478.16 4676.23
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 11 1 QTDYLTGTD ETDYLTGTD PickPocket 11355.63 18882.64 1.663 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 11355.63 18882.64 1.663 NA NA 18882.64 11355.63
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 4 8 GTLKFNPQT GTLKFNPET PickPocket 11986.87 9047.59 0.755 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 11986.87 9047.59 0.755 NA NA 9047.59 11986.87
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 7 5 KFNPQTDYL KFNPETDYL PickPocket 12117.27 14722.66 1.215 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 15232.4 16891.629999999997 1.109 19060.6 18347.53 14722.66 12117.27
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 4 8 GTLKFNPQT GTLKFNPET PickPocket 12930.01 13070.67 1.011 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 26831.14 27035.22 1.008 40999.77 40732.27 13070.67 12930.01
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 7 5 KFNPQTDYLT KFNPETDYLT PickPocket 13070.67 13212.86 1.011 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 13070.67 13212.86 1.011 NA NA 13212.86 13070.67
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 3 9 AGTLKFNPQ AGTLKFNPE PickPocket 18082.85 17888.25 0.989 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 30892.395 30886.785 1.0 43885.32 43701.94 17888.25 18082.85
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 5 7 TLKFNPQTD TLKFNPETD PickPocket 18082.85 17316.93 0.958 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 29459.19 29409.41 0.998 41501.89 40835.53 17316.93 18082.85
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 8 4 FNPQTDYLT FNPETDYLT PickPocket 19295.7 17505.31 0.907 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 19295.7 17505.31 0.907 NA NA 17505.31 19295.7
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 3 9 AGTLKFNPQT AGTLKFNPET PickPocket 21734.48 21970.92 1.011 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 33658.015 33866.91 1.006 45762.9 45581.55 21970.92 21734.48
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 9 3 NPQTDYLTG NPETDYLTG PickPocket 21970.92 25289.19 1.151 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 31408.965 33193.335 1.057 41097.48 40847.01 25289.19 21970.92
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 5 7 TLKFNPQTD TLKFNPETD PickPocket 22695.78 24218.04 1.067 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 22695.78 24218.04 1.067 NA NA 24218.04 22695.78
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 4 8 GTLKFNPQTD GTLKFNPETD PickPocket 28178.94 28178.94 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 28178.94 28178.94 1.0 NA NA 28178.94 28178.94
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 7 5 KFNPQTDYLT KFNPETDYLT PickPocket 30068.96 33869.37 1.126 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 32199.935 34522.025 1.072 35174.68 34330.91 33869.37 30068.96
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 9 3 NPQTDYLTG NPETDYLTG PickPocket 30726.73 50000.0 1.627 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 30726.73 50000.0 1.627 NA NA 50000.0 30726.73
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 11 1 QTDYLTGTDG ETDYLTGTDG PickPocket 31398.89 50000.0 1.592 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 31398.89 50000.0 1.592 NA NA 50000.0 31398.89
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 6 6 LKFNPQTDYL LKFNPETDYL NetMHC 33452.35 33914.48 1.014 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 41726.175 41957.240000000005 1.006 33914.48 33452.35 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 8 4 FNPQTDYLTG FNPETDYLTG PickPocket 33869.37 31060.99 0.917 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 33869.37 31060.99 0.917 NA NA 31060.99 33869.37
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 6 6 LKFNPQTDYL LKFNPETDYL PickPocket 34986.78 36931.66 1.056 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 34986.78 36931.66 1.056 NA NA 36931.66 34986.78
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 11 1 QTDYLTGTD ETDYLTGTD NetMHC 41972.45 42738.65 1.018 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 45986.225 46369.325 1.008 42738.65 41972.45 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 6 6 LKFNPQTDY LKFNPETDY NetMHC 43715.19 43923.32 1.005 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 46059.14 45138.125 0.98 43923.32 43715.19 46352.93 48403.09
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 5 7 TLKFNPQTDY TLKFNPETDY NetMHC 44629.45 44915.24 1.006 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 47314.725 47457.62 1.003 44915.24 44629.45 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 9 10 2 PQTDYLTGT PETDYLTGT NetMHC 44982.35 45597.84 1.014 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 47491.175 47798.92 1.006 45597.84 44982.35 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 4 8 GTLKFNPQTD GTLKFNPETD NetMHC 45866.52 46007.66 1.003 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 47933.26 48003.83 1.001 46007.66 45866.52 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 2 10 IAGTLKFNPQ IAGTLKFNPE NetMHC 46065.46 46172.24 1.002 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 48032.73 48086.12 1.001 46172.24 46065.46 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 9 3 NPQTDYLTGT NPETDYLTGT NetMHC 46148.75 46224.73 1.002 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 48074.375 48112.365000000005 1.001 46224.73 46148.75 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 11 1 QTDYLTGTDG ETDYLTGTDG NetMHC 46570.09 46809.05 1.005 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 48285.045 48404.525 1.002 46809.05 46570.09 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-E*01:01 10 10 2 PQTDYLTGTD PETDYLTGTD NetMHC 46719.99 46966.32 1.005 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 48359.995 48483.16 1.003 46966.32 46719.99 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 3 9 AGTLKFNPQ AGTLKFNPE PickPocket 46857.18 43439.36 0.927 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 46857.18 43439.36 0.927 NA NA 43439.36 46857.18
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 10 2 PQTDYLTGT PETDYLTGT PickPocket 46857.18 50000.0 1.067 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 46857.18 50000.0 1.067 NA NA 50000.0 46857.18
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 2 10 IAGTLKFNPQ IAGTLKFNPE PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 3 9 AGTLKFNPQT AGTLKFNPET PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 5 7 TLKFNPQTDY TLKFNPETDY PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 9 6 6 LKFNPQTDY LKFNPETDY PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 9 3 NPQTDYLTGT NPETDYLTGT PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 41920894 41920895 G C ENST00000216254 ENSG00000100412 missense E/Q 510 ACO2 ENST00000216254.4:c.1528G>C ENSP00000216254.4:p.Glu510Gln HLA-G*01:09 10 10 2 PQTDYLTGTD PETDYLTGTD PickPocket 50000.0 50000.0 1.0 129 0.2713178294573643 NA NA NA NA 38.5035 35.4301 50000.0 50000.0 1.0 NA NA 50000.0 50000.0
22 38027027 38027028 C G ENST00000343632 ENSG00000100083 missense P/A 484 GGA1 ENST00000343632.4:c.1450C>G ENSP00000341344.4:p.Pro484Ala HLA-E*01:01 9 11 1 ARPPQQPVP PRPPQQPVP PickPocket 1654.99 4242.33 2.563 230 0.4869565217391304 NA NA NA NA 20.6372 10.5565 6693.895 10556.225 1.577 16870.12 11732.8 4242.33 1654.99
22 38027027 38027028 C G ENST00000343632 ENSG00000100083 missense P/A 484 GGA1 ENST00000343632.4:c.1450C>G ENSP00000341344.4:p.Pro484Ala HLA-E*01:01 9 8 4 PEPARPPQQ PEPPRPPQQ PickPocket 2873.7 2812.19 0.979 230 0.4869565217391304 NA NA NA NA 20.6372 10.5565 10491.195 7573.6 0.722 12335.01 18108.69 2812.19 2873.7
22 38027027 38027028 C G ENST00000343632 ENSG00000100083 missense P/A 484 GGA1 ENST00000343632.4:c.1450C>G ENSP00000341344.4:p.Pro484Ala HLA-E*01:01 9 4 8 HTVSPEPAR HTVSPEPPR PickPocket 5210.57 5154.5 0.989 230 0.4869565217391304 NA NA NA NA 20.6372 10.5565 22958.865 22465.835 0.979 39777.17 40707.16 5154.5 5210.57
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8 changes: 4 additions & 4 deletions tools/pvacseq/coverage_filter.py
View file
Expand Up @@ -42,14 +42,14 @@ def define_parser():
parser.add_argument(
'--tdna-vaf', type=int,
help="Tumor DNA VAF Cutoff. Sites above this cutoff will be considered. "
+ "Default: 0.4",
default=0.4
+ "Default: 0.25",
default=0.25
)
parser.add_argument(
'--trna-vaf', type=int,
help="Tumor RNA VAF Cutoff. Sites above this cutoff will be considered. "
+ "Default: 0.4",
default=0.4
+ "Default: 0.25",
default=0.25
)
parser.add_argument(
'--expn-val', type=int,
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4 changes: 2 additions & 2 deletions utils/pvacapi/config/swagger.yaml
View file
Expand Up @@ -352,12 +352,12 @@ paths:
in: "formData"
description: "Tumor DNA VAF Cutoff: Sites above this cutoff will be considered"
type: "number"
default: 0.4
default: 0.25
- name: "trna_vaf"
in: "formData"
description: "Tumor RNA VAF Cutoff: Sites above this cutoff will be considered"
type: "number"
default: 0.4
default: 0.25
- name: "expn_val"
in: "formData"
description: "Gene and Transcript Expression cutoff: Sites above this cutoff will be considered"
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4 changes: 2 additions & 2 deletions utils/pvacapi/controllers/staging.py
View file
Expand Up @@ -146,8 +146,8 @@ def staging(parameters):
'tdna_cov': parameters.pop('tdna_cov', 10), # tdna_cov
'trna_cov': parameters.pop('trna_cov', 10), # trna_cov
'normal_vaf': parameters.pop('normal_vaf', 0.02), # normal_vaf
'tdna_vaf': parameters.pop('tdna_vaf', 0.4), # tdna_vaf
'trna_vaf': parameters.pop('trna_vaf', 0.4), # trna_vaf
'tdna_vaf': parameters.pop('tdna_vaf', 0.25), # tdna_vaf
'trna_vaf': parameters.pop('trna_vaf', 0.25), # trna_vaf
'expn_val': parameters.pop('expn_val', 1), # expn_val
'net_chop_threshold': parameters.pop('net_chop_threshold', 0.5),
'fasta_size': parameters.pop('fasta_size', 200),
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