P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset
- vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every computed field identical in 2138/2141 samples; the 3 others trace back to the single-locus raw-intensity rule (K-009); sex rule 1 matches all - AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3: new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3, legacy statistics); the sample summary keeps the real statistics - NaN sign canonicalised to the x86 pattern (K-014); report P4.md
This commit is contained in:
kemal committed
1 parent
7fb3967c3f
commit
f469c97917
9 files changed
+792
-29
No files matched your search
@@ -0,0 +1,615 @@
|
||||
{
|
||||
"n_gtc": 2141,
|
||||
"n_compared": 2141,
|
||||
"errors": [],
|
||||
"byte_identical": 0,
|
||||
"samples_with_no_field_diff": 0,
|
||||
"samples_with_field_diff": {
|
||||
"gc10": 2141,
|
||||
"gc50": 2141,
|
||||
"num_calls": 2141,
|
||||
"num_no_calls": 2141,
|
||||
"slide_identifier": 2141,
|
||||
"raw_x": 1,
|
||||
"genotypes": 3,
|
||||
"genotype_scores": 3,
|
||||
"base_calls": 3,
|
||||
"call_rate": 2,
|
||||
"logr_dev": 3,
|
||||
"raw_y": 2,
|
||||
"normalization_transforms": 2
|
||||
},
|
||||
"genotype_diff_loci_total": 5,
|
||||
"score_diff_loci_total": 18229,
|
||||
"max_score_abs_diff": 0.9426311254501343,
|
||||
"cluster_files": [
|
||||
"HumanOmni2.5-4v1-Multi_B.egt"
|
||||
],
|
||||
"sex_agreement_by_version": {
|
||||
"1": 2141,
|
||||
"2": 2129
|
||||
},
|
||||
"ref_sex_counts": {
|
||||
"M": 1054,
|
||||
"F": 1087,
|
||||
"U": 0
|
||||
},
|
||||
"examples": [
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511011/5426511011_R01C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6847535967826843",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2433210",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"16790",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511011'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Wednesday, August 25, 2010 7:11:03 PM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511011/5426511011_R02C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6842713356018066",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2436202",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"13798",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511011'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Wednesday, August 25, 2010 7:24:37 PM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511011/5426511011_R03C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6842615604400635",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435069",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14931",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511011'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Wednesday, August 25, 2010 7:37:41 PM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511011/5426511011_R04C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6863988637924194",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497668504714966",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435856",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14144",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511011'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Wednesday, August 25, 2010 7:45:50 PM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511013/5426511013_R01C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6843520402908325",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2434354",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"15646",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511013'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 12:08:26 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511013/5426511013_R02C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.685818076133728",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497965335845947",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2439588",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"10412",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511013'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 12:22:41 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511013/5426511013_R03C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6856454014778137",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497673273086548",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2442131",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"7869",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511013'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 12:37:24 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511013/5426511013_R04C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6856228113174438",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2440841",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"9159",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511013'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 12:46:33 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511028/5426511028_R01C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6833689212799072",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8496665954589844",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435388",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14612",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511028'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 8:13:23 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511028/5426511028_R02C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6857903599739075",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435889",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14111",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511028'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 8:28:43 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511028/5426511028_R03C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6847374439239502",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497611880302429",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435026",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14974",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511028'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 8:40:16 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511028/5426511028_R04C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6849170923233032",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497409820556641",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2433211",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"16789",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511028'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 8:50:08 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511029/5426511029_R01C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.683781087398529",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497233390808105",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2439124",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"10876",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511029'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 9:12:02 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511029/5426511029_R02C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6832002401351929",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8497028946876526",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2437630",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"12370",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511029'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "M",
|
||||
"2": "M"
|
||||
},
|
||||
"sex_ref": "M",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 9:26:14 AM"
|
||||
}
|
||||
},
|
||||
{
|
||||
"gtc": "/work/omni/data/5426511029/5426511029_R03C01.gtc",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"field_diffs": {
|
||||
"gc10": [
|
||||
"0.6829559803009033",
|
||||
"0.0"
|
||||
],
|
||||
"gc50": [
|
||||
"0.8496484756469727",
|
||||
"0.0"
|
||||
],
|
||||
"num_calls": [
|
||||
"2435690",
|
||||
"0"
|
||||
],
|
||||
"num_no_calls": [
|
||||
"14310",
|
||||
"0"
|
||||
],
|
||||
"slide_identifier": [
|
||||
"'5426511029'",
|
||||
"''"
|
||||
]
|
||||
},
|
||||
"sex_by_version": {
|
||||
"1": "F",
|
||||
"2": "F"
|
||||
},
|
||||
"sex_ref": "F",
|
||||
"byte_identical": false,
|
||||
"ref_layout_canonical": true,
|
||||
"metadata": {
|
||||
"autocall_version": "1.6.2.2",
|
||||
"cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
|
||||
"imaging_date": "Thursday, August 26, 2010 9:40:16 AM"
|
||||
}
|
||||
}
|
||||
],
|
||||
"params": {
|
||||
"norm_version": "1.1.2",
|
||||
"sex_version": 1
|
||||
},
|
||||
"seconds": 1174.6,
|
||||
"passed": false
|
||||
}
|
||||
Reference in new issue
Block a user