view parse.conf @ 0:b77ab858eac1 draft

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<filter>
SNV_FILTER
SNV_FILTER_NUM
CHR
</filter>

<files>
ROOT
CNV
SNV
MART 
CIRCOS 
</files>

<fields>
<cnv>
key = sample,chr
0   = sample
1   = chr
2   = start
3   = end
5   = avg
6   = category:lc
</cnv>

<sv>
key = id,sample
4   = chr
5   = start
6   = end
8   = type:lc
15  = sample
47  = id
53  = aa
</sv>

<genes>
key = chr
0   = id
2   = end
3   = start
4   = chr
5   = name
</genes>
</fields>

<cnv>
filter     = yes
<types>
amp   = 20
gain  = 15
neut  = 0
hetd  = 10
homd  = 5
hlamp = 0
</types>
</cnv>

<sv>
filter     = yes
top_damage_only   = yes
<types>
nonsense_mutation = 35
frame_shift_del   = 30
frame_shift_ins   = 25
in_frame_del      = 20
in_frame_ins      = 15
splice_site       = 10
nonstop_mutation  = 5
missense_mutation = 1
</types>
</sv>