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config.yaml
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config.yaml
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bucket : egglimpute
tmp_dir: /scratch/tmp
samples : [
'A1543', 'A2068', 'A2071','A2085', 'A4416', 'A5659', 'A5964', 'ADM9', 'ADR419', 'ADR420', 'ADR421', 'ADR422', 'ADR423', 'ADR424', 'ADR425', 'ARAB0016A', 'ARAB0017A', 'ARAB0018A', 'ARAB0019A',
#'ARAB0020A', 'ARAB0034A', 'ARAB0035A', 'ARAB0036A', 'ARAB0132A', 'ARAB0133A', 'ARAB0134A', 'ARAB0135A', 'ARAB0136A', 'ARAB0141A', 'BAVA0183A', 'BROOKS2174', 'BROOKS3147', 'BROOKS3148', 'BW01',
#'CLDB65664', 'CLDB65665', 'CLDB65666', 'CON15', 'CON26', 'CON3', 'CON40', 'CUTR0137A', 'CUTR0138A', 'ERR1397962', 'ERR1397965', 'ERR1527951', 'ERR1527966', 'ERR1527967', 'ERR1527968', 'ERR1527969',
#'ERR1527970', 'ERR1527972', 'ERR1545178', 'ERR1545179', 'ERR1545180', 'ERR1545181', 'ERR1545182', 'ERR1545187', 'ERR1545188', 'ERR1545189', 'ERR1545190', 'ERR793393', 'ERR863167', 'ERR868003',
#'ERR868004', 'ERR953413', 'ERR982786', 'ERR982794', 'FJOR0142A', 'FRMO0037A', 'FRMO0041A', 'FRMO0042A', 'FRMO0043A', 'FRMO0044A', 'FRMO0045A', 'FRMO0046A', 'FRMO0047A', 'FRMO0048A', 'FRMO0049A',
#'FRMO0050A', 'FRMO0051A', 'FRMO0052A', 'FRMO0053A', 'FRMO0054A', 'FRMO0055A', 'FRMO0056A', 'FRMO0057A', 'FRMO0058A', 'FRMO0059A', 'FRMO0060A', 'FRMO0061A', 'FRMO0062A', 'FRMO0063A', 'FRMO0064A',
#'FRMO0065A', 'FRMO0066A', 'FRMO0067A', 'FRMO0068A', 'FRMO0069A', 'FRTR0023A', 'FRTR0024A', 'FRTR0025A', 'FRTR0026A', 'FRTR0027A', 'FRTR0028A', 'FRTR0029A', 'FRTR0030A', 'FRTR0139A', 'FRTR0140A',
#'HAFL0015A', 'HANO0172A', 'HF13B', 'HF13C', 'HF13D', 'HF14A', 'HF14C', 'HF15A', 'HOLS0173A', 'HOLS0174A', 'HOLS0175A', 'ICEL0143A', 'ICEL0144A', 'IT3', 'IT4', 'K743', 'K744', 'K745', 'K746', 'K747',
#'LIPI0186A', 'LIPI0187A', 'LIPI0188A', 'LIPI0189A', 'M1005', 'M1009', 'M1012', 'M1027', 'M1048', 'M10638', 'M10639', 'M10640', 'M10641', 'M10642', 'M10643', 'M10644', 'M10645', 'M10646', 'M10647',
#'M10648', 'M10649', 'M10652', 'M10653', 'M10656', 'M10657', 'M10658', 'M10659', 'M10661', 'M10662', 'M10663', 'M10664', 'M10665', 'M10666', 'M10667', 'M10668', 'M10672', 'M10673', 'M10675', 'M10676',
#'M10677', 'M10678', 'M10679', 'M10681', 'M10682', 'M10683', 'M10684', 'M10990', 'M10991', 'M10992', 'M10993', 'M10994', 'M10995', 'M10996', 'M10997', 'M10998', 'M10999', 'M11000', 'M11001', 'M11002',
#'M11003', 'M11004', 'M11005', 'M11006', 'M11007', 'M11008', 'M11009', 'M11010', 'M11011', 'M11012', 'M11013', 'M11014', 'M11015', 'M11016', 'M11017', 'M11018', 'M11019', 'M11020', 'M11021', 'M11022',
#'M11023', 'M11024', 'M11025', 'M1433', 'M1458', 'M1503', 'M1505', 'M1506', 'M1507', 'M1510', 'M1514', 'M1516', 'M1518', 'M1519', 'M1542', 'M1545', 'M1552', 'M1555', 'M1556', 'M1557', 'M1559', 'M1561',
#'M1563', 'M1565', 'M1568', 'M1570', 'M1571', 'M1579', 'M1581', 'M1583', 'M1930', 'M1931', 'M1932', 'M1937', 'M1939', 'M1941', 'M1942', 'M1944', 'M1946', 'M1964', 'M1966', 'M1967', 'M1968', 'M1970',
#'M2023', 'M2025', 'M2039', 'M2044', 'M2060', 'M2068', 'M315', 'M316', 'M367', 'M369', 'M4409', 'M4410', 'M4411', 'M4418', 'M4435', 'M4437', 'M4438', 'M4440', 'M4467', 'M4472', 'M4475', 'M4476', 'M4486',
#'M4487', 'M4488', 'M4493', 'M4513', 'M4514', 'M4515', 'M4527', 'M4537', 'M4540', 'M4541', 'M4546', 'M466', 'M467', 'M468', 'M469', 'M470', 'M472', 'M473', 'M475', 'M476', 'M477', 'M478', 'M479', 'M4809',
#'M4814', 'M4815', 'M4826', 'M4869', 'M487', 'M4990', 'M5005', 'M5112', 'M5256', 'M5259', 'M5260', 'M5269', 'M5271', 'M5287', 'M5300', 'M5304', 'M5306', 'M6105', 'M6115', 'M6117', 'M6122', 'M6130',
#'M6137', 'M6138', 'M6163', 'M6166', 'M6167', 'M6175', 'M6182', 'M6184', 'M6187', 'M6188', 'M6194', 'M6202', 'M6212', 'M6231', 'M6252', 'M6253', 'M6287', 'M6294', 'M6296', 'M6304', 'M6337', 'M6449',
#'M6462', 'M6468', 'M6482', 'M6536', 'M6539', 'M6558', 'M6566', 'M6572', 'M6576', 'M6577', 'M6579', 'M6598', 'M6660', 'M6682', 'M6798', 'M6807', 'M6813', 'M6850', 'M6911', 'M6991', 'M6993', 'M7572',
#'M7645', 'M7681', 'M7700', 'M7721', 'M7723', 'M7756', 'M7761', 'M7762', 'M7763', 'M7789', 'M7814', 'M7818', 'M7836', 'M7844', 'M8457', 'M8458', 'M8459', 'M8460', 'M8461', 'M8463', 'M8464', 'M8465',
#'M8466', 'M8467', 'M8679', 'M8738', 'M968', 'M977', 'M989', 'M992', 'MONG0153A', 'OLDE0176A', 'OLDE0177A', 'PRZE0150A', 'PRZE0151A', 'PRZE0152A', 'PRZE0154A', 'PRZE0155A', 'PRZE0156A', 'PRZE0157A',
#'PRZE0158A', 'PRZE0159A', 'PRZE0160A', 'PRZE0161A', 'PRZE0162A', 'RAO310', 'RAO441', 'SATR0021A', 'SATR0022A', 'SRR1046129', 'SRR1046135', 'SRR1046147', 'SRR1046151', 'SRR1048526', 'SRR1167052',
#'SRR1167053', 'SRR1167093', 'SRR1167108', 'SRR1167109', 'SRR1167110', 'SRR1167891', 'SRR1167892', 'SRR1167893', 'SRR1564419', 'SRR1564421', 'SRR1564422', 'SRR1564423', 'SRR2102500', 'SRR2102896',
#'SRR2103372', 'SRR2142163', 'SRR2142269', 'SRR2142311', 'SRR2142313', 'SRR3726219', 'SRR388336', 'SRR388337', 'SRR3900279', 'SRR3900280', 'SRR3900281', 'SRR3900282', 'SRR3900283', 'SRR3900284',
#'SRR3900285', 'SRR3900286', 'SRR3900287', 'SRR3900288', 'SRR3900289', 'SRR3900290', 'SRR3900298', 'SRR3900315', 'SRR3900336', 'SRR3900337', 'SRR3900338', 'SRR3900339', 'SRR3900340', 'SRR3900341',
#'SRR3900342', 'SRR3900343', 'SRR3900344', 'SRR3900345', 'SRR3900346', 'SRR3900347', 'SRR3900348', 'SRR3900349', 'SRR3900350', 'SRR3900351', 'SRR3900352', 'SRR3900353', 'SRR3952018', 'SRR4054238',
#'SRR4054239', 'SRR4054240', 'SRR4054241', 'SRR4054242', 'SRR4054277', 'SRR4054279', 'SRR505867', 'SRR515202', 'SRR515203', 'SRR515204', 'SRR515205', 'SRR515206', 'SRR515208', 'SRR515209', 'SRR515211',
#'SRR515212', 'SRR515213', 'SRR515214', 'SRR515215', 'SRR515216', 'SRR515217', 'SRR515218', 'SRR516104', 'SRR516118', 'SRR526907', 'SRR526908', 'SRR526909', 'SRR527519', 'SRR527520', 'SRR527521',
#'SRR527527', 'SRR527528', 'SRR527799', 'SRR527800', 'SRR527801', 'SRR527802', 'SRR527803', 'SRR527804', 'SRR527805', 'SRR527806', 'SRR527807', 'SRR527809', 'SRR527825', 'SRR5755256', 'SRR6175104',
#'SRR6175105', 'SRR6175106', 'SRR6175107', 'SRR6175108', 'SRR6175109', 'SRR6175110', 'SRR6175111', 'SRR6374293', 'SRR641364', 'SRR641365', 'SRR641366', 'SRR641367', 'STAN0149A', 'TRAK0178A',
#'TRAK0179A', 'TWILIGHT', 'UKH3', 'WEST180A', 'WEST181A', 'YAKU0163A', 'YAKU0164A', 'YAKU0165A', 'YAKU0166A', 'YAKU0167A', 'YAKU0168A', 'YAKU0169A', 'YAKU0170A', 'YAKU0171A'
]
contigs:
# Autosomes
- NC_009144_3 # chr1
- NC_009145_3 # chr2
- NC_009146_3 # chr3
- NC_009147_3 # chr4
- NC_009148_3 # chr5
- NC_009149_3 # chr6
- NC_009150_3 # chr7
- NC_009151_3 # chr8
- NC_009152_3 # chr9
- NC_009153_3 # chr10
- NC_009154_3 # chr11
- NC_009155_3 # chr12
- NC_009156_3 # chr13
- NC_009157_3 # chr14
- NC_009158_3 # chr15
- NC_009159_3 # chr16
- NC_009160_3 # chr17
- NC_009161_3 # chr18
- NC_009162_3 # chr19
- NC_009163_3 # chr20
- NC_009164_3 # chr21
- NC_009165_3 # chr22
- NC_009166_3 # chr23
- NC_009167_3 # chr24
- NC_009168_3 # chr25
- NC_009169_3 # chr26
- NC_009170_3 # chr27
- NC_009171_3 # chr28
- NC_009172_3 # chr29
- NC_009173_3 # chr30
- NC_009174_3 # chr31
- NC_009175_3 # chrX
# Other somes
#- NC_001640_1 # Mitochindria
#- unplaced # Unplaced/Chrunk
caller:
- gatk
- bcftools
maf:
# - MAF01
- MAF005
fltr:
- biallelic
lsts:
- MNEc2M
- MNEc670k
- SNP70
- SNP50
vqsr:
# - 100
- VQSR995
# - 99