forked from cbirdlab/dDocentHPC
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.4.all
207 lines (132 loc) · 7.02 KB
/
config.4.all
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
Number of Processors (Auto, 1, 2, 3, ..., n threads) cbirdq=40 normal=20
40
Maximum Memory (1G,2G,..., 256G) G=gigabytes
230G
----------Settings for Trimming----------------------------------------------------
Trimming (yes,no)
no
TRIM_LENGTH_ASSEMBLY
146
SEED_ASSEMBLY (applies to trim for assembly and mapping)
2
PALIMDROME_ASSEMBLY (applies to trim for assembly and mapping)
30
SIMPLE_ASSEMBLY (applies to trim for assembly and mapping)
10
windowSize_ASSEMBLY (applies to trim for assembly and mapping)
20
windowQuality_ASSEMBLY (applies to trim for assembly and mapping)
10
TRAILING_ASSEMBLY
10
TRIM_LENGTH_MAPPING
75
LEADING_MAPPING
15
TRAILING_MAPPING
15
----------Settings for FixStacks---------------------------------------------------
FixStacks (yes,no) Demultiplexing with stacks introduces anomolies. This removes them.
no
----------Settings for de novo assembling the reference genome--------------------
Assembly? (yes or no)
no
Type_of_Assembly (PE, SE, OL, RPE)
PE
Clustering_Similarity% (0-1)
0.9
HPC, Get graphs for cutoffs, then stop? (yes or no)
no
Manually set cutoffs? (yes or no) If yes is selected then dDocent will prompt you to enter cutoff values.
no
Cutoff1
25
Cutoff2
10
----------Settings for mapping the reads------------------------------------------
Make sure the cutoffs above match your reference!
Mapping_Reads? (yes or no)
no
Mapping_Match_Value (integer) bwa mem -A
1
Mapping_MisMatch_Value (integer) bwa mem -B
6
Mapping_GapOpen_Penalty (integer) bwa mem -O
10
Mapping_Minimum_Alignment_Score (integer) bwa mem -T
50
Mapping_Clipping_Penalty (integer,integer) bwa mem -L
30,5
----------Settings for filtering mapping alignments (BAM FILTERING)---------------
Filter_Mapped_Read_Alignments? (yes or no)
no
Mapping_Min_Quality (integer) samtools view -q
20
Remove_unmapped_reads? (yes,no) samtools view -F 4
no
Remove_read_pair_if_one_is_unmapped? (yes,no) samtools view -F 8
yes
Remove_secondary_alignments? (yes,no) samtools view -F 256
yes
Remove_reads_not_passing_platform_vendor_filters (yes,no) samtools view -F 512
no
Remove_PCR_or_optical_duplicates? (yes,no) samtools view -F 1024
no
Remove_supplementary_alignments? (yes,no) samtools view -F 2048
no
Keep_only_properly_aligned_read_pairs? (yes,no) samtools view -f 2 Set to no if OL mode
yes
Custom_samtools_view_F_bit_value? (integer) samtools view -F, performed separately from the above
0
Custom_samtools_view_f_bit_value? (integer) samtools view -f, performed separately from the above
0
Remove_reads_with_excessive_soft_clipping? (no, integer by 10s) minimum number of soft clipped bases in a read that is unacceptable
20
Remove_reads_with_alignment_score_below (integer by 10s) Not currently fuctional
50
Remove_reads_orphaned_by_filters? (yes,no)
yes
----------Settings for variant calling--------------------------------------------
Calling_SNPs?
yes
Is the data pooled? (yes or no) If yes, a pool of individuals is assumed to be the statistical unit of observation
no
If the data is pooled, will you provide a copy number variation (cnv) *.bed file with the ploidy of each pool? (no for filename.bed) freebayes -J or freebayes -K , if yes, then you have to put a file with the specified name in the the genotyping directory with the following format: popmap_column_1 ploidy
no
If no cnv file is provided, then what is the ploidy of the samples (integer) -p ?
2
Use_Best_N_Alleles (integer) freebayes -n , reduce the number of alleles considered to n, zero means all, set to 2 or more if you run out of memory
0
Minimum_Mapping_Quality (integer) freebayes -m
30
Minimum_Base_Quality (integer) freebayes -q
20
Haplotype_Length (-1, 3, or integer) freebayes -E If -1, then clumping/mnps/etc is disabled. Can be set up to half the read length, or more.
-1
Min_Repeat_Entropy (0, 1, or integer) freebayes --min-repeat-entropy
0
Min_Coverage (integer) freebayes --min-coverage Require at least this coverage to process a site
10
Min_Alternate_Fraction (0.2, decimal) freebayes -F If your individuals are barcoded, then use 0.2. If your data is pooled, then set based upon ~ 1/(numIndivids * ploidy) and average depth of coverage
0.375
Min_Alternate_Count (integer) freebayes -C Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 2
20
Min_Alternate_Total (integer) freebayes -G Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. default: 1
20
Read_Max_Mismatch_Fraction (decimal 0-1) freebayes -z Exclude reads with more than N [0,1] fraction of mismatches
0.33
0.33 freebayes -z --read-max-mismatch-fraction Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold default: 1.0
20 freebayes -C --min-alternate-count Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 2
30 freebayes ~3 ~~min-alternate-qsum This value is the mean base quality score for alternate reads and will be multiplied by -C to set -3. Description of -3: Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 2
20 freebayes -G --min-alternate-total Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. default: 1
20 freebayes -Q --mismatch-base-quality-threshold Count mismatches toward --read-mismatch-limit if the base quality of the mismatch is >= Q. default: 10
30 freebayes -U --read-mismatch-limit Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold. default: ~unbounded
30 freebayes -$ --read-snp-limit Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold. default: ~unbounded
20 freebayes -e --read-indel-limit Exclude reads with more than N separate gaps. default: ~unbounded
no freebayes -w --hwe-priors-off (no|yes)Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency.
no freebayes -V --binomial-obs-priors-off (no|yes)Disable incorporation of prior expectations about observations. Uses read placement probability, strand balance probability, and read position (5'-3') probability.
no freebayes -a --allele-balance-priors-off (no|yes)Disable use of aggregate probability of observation balance between alleles as a component of the priors.
no freebayes --no-partial-observations Exclude observations which do not fully span the dynamically-determined detection window. (default, use all observations, dividing partial support across matching haplotypes when generating haplotypes.)
----------Misc settings-----------------------------------------------------------
Email
tamucc.edu