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biopet.biopet
Commits
ffaadd57
Commit
ffaadd57
authored
Nov 29, 2016
by
Peter van 't Hof
Browse files
Adding ref ALT
parent
238fb305
Changes
1
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Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
ffaadd57
...
...
@@ -69,6 +69,7 @@ object MpileupToVcf extends ToolCommand {
val
writer
=
new
PrintWriter
(
commandArgs
.
output
)
writer
.
println
(
"##fileformat=VCFv4.1"
)
writer
.
println
(
"##ALT=<ID=REF,Description=\"Placeholder if location has no ALT alleles\">"
)
writer
.
println
(
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">"
)
writer
.
println
(
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">"
)
writer
.
println
(
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">"
)
...
...
@@ -190,7 +191,7 @@ object MpileupToVcf extends ToolCommand {
}
left
-=
ad
(
max
)
}
writer
.
println
(
Array
(
chr
,
pos
,
"."
,
ref
.
toUpperCase
,
alt
.
mkString
(
","
),
"."
,
"."
,
info
.
mkString
(
";"
),
writer
.
println
(
Array
(
chr
,
pos
,
"."
,
ref
.
toUpperCase
,
(
if
(
alt
.
nonEmpty
)
alt
.
mkString
(
","
)
else
"<REF>"
)
,
"."
,
"."
,
info
.
mkString
(
";"
),
"GT:"
+
format
.
keys
.
mkString
(
":"
),
gt
.
sortWith
(
_
<
_
).
mkString
(
"/"
)
+
":"
+
format
.
values
.
mkString
(
":"
)
).
mkString
(
"\t"
))
}
...
...
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