Generated simulated trio dataset.

data/README

-This is where we store all raw data.
-
-Use git annex to track the data.
-
-Describe the data (by editing this file):
-- What type of data:
-  - Sequencing centre.
-  - Platform.
-  - Molecular type (RNA, DNA).
-  - Capture kit.
-- Owner of the data (client).
-- Who gathered the data.
+Platform       : Illumina HiSeq (simulated)
+Molecular type : DNA
+Capture kit    : custom
+
+Owner: J.F.J. Laros <J.F.J. Laros@lumc.nl>
+
+Gathered by: J.F.J. Laros <J.F.J. Laros@lumc.nl>
+
+Notes:
+python makeFastq.py mutate -o out_half -l 100 -n 330000 -i input.txt
+python makeFastq.py mutate -o out -l 100 -n 660000 -i input.txt
+
+child_1.fq, child_2.fq, child.txt:
+python ../src/sim-reads/sim-reads/makeFastq.py mutate -o child -l 100 -n 660000 -i variants.txt
+
+reference.fa:
+fastools get -s 136800000 -p 139000000 reference.fa NC_000008.10 j.f.j.laros@lumc.nl
+
+father_1.fq, father_2.fq, father.txt:
+python ../src/sim-reads/sim-reads/makeFastq.py local -o father -l 100 -n 660000 -r reference.fa

data/child.txt

+UD_129077402355: NC_000008.10:136800000_139000000
+
+1660001C>A
+1661001A>T
+1661006T>A
+1662001C>T
+1662005A>G
+1662010A>T
+1663001C>T
+1663005T>G
+1663010A>G
+1663017T>A
+1664001G>C
+1664003T>G
+1664005T>C
+1664007A>C
+1664010A>T
+1664013A>G
+1664017G>T
+1665004del
+1665102_1665103del
+1665203_1665205del
+1665302_1665305del
+1665401_1665406del
+1665501_1665509del
+1665602_1665616del
+1665701_1665735del
+1666002dup
+1666202_1666203dup
+1666403_1666407dup
+1666602_1666611dup
+1666802_1666826dup
+1667004_1667103dup
+1667902_1668601dup
+291001_291002insT
+291201_291202insTA
+291401_291402insTACTC
+291605_291606insCATAGCTACT
+291801_291802insTACTCATAGCTTCCTGTAATCTATT
+292001_292002insTACTCATAGCTTCCTGTAATCTATTTTAGGAGCAATCAAAAATATTTTGAACCATGTCCTCTTCCACTTAGCTTAAGTATGCAATGGAGTATAGTGTCTG
+293001_293002insTACTCATAGCTTCCTGTAATCTATTTTAGGAGCAATCAAAAATATTTTGAACCATGTCCTCTTCCACTTAGCTTAAGTATGCAATGGAGTATAGTGTCTGCCTTTATTAATTCTAATAACTAGTCTCACTGTCCCAAGCCTACTAAATATTTGATTATATGATCCATCTAGTTTCTGTTCCTAGAACCGTGAGAAGTGGAGTGAGAGGAGAGCATTTTGTTTATCATTTAACTCTCAGAGACAGGAATAGGTGTATCCTTGTAAGTGAGAATGAAATCCTGAAGGCAGGGAGTAGGAAATATGGTGTGATTCAGTTCCTCATCTTGAAGAATATCTCCTAAGTTGGCTCTGAAAAGCTGTAGGTGTAATTCTAGCCCCTTGATAATTAGTATTGCCCTATCAGCAGAGGGTGGACATTATGCAAAAAAAAAAAAAAAAAAAAAAAAAACTGGAGAAAATTAAATTGGATGTGGAGTGCCTCCTTTTCTTAAAAAAACAACTTTATTGAGGTGTTATTGATAGACAAAGAACTGCACATATTTCATATATACCATTTGATAAGTTTTAACCTTTGCAAAGACTCATGATACCATTGCCACAACCTAGGTCATCGATATGTCCAACACATCCCTAAGTTTCCTTGTGTTTCTTTGATTTCGTTTTTTGTTTCTGTTTTTATTTTTTGTGGTTCCAACATTTA
+316001C>A
+316002T>G
+316101A>G
+316102_316104del
+317001_317002inv
+317103_317108inv
+317201_317205inv
+317301_317325inv
+317501_317600inv
+319002_319699inv
+320001A>G
+320006del
+320101A>G
+320105dup
+320201T>A
+320207dup

data/child_1.fq

+../.git/annex/objects/vj/M4/SHA256E-s141128895--322ee413506208c7c5c32c8bd91c4d9948a0c802d4bd08f0672cca5f316a61ad.fq/SHA256E-s141128895--322ee413506208c7c5c32c8bd91c4d9948a0c802d4bd08f0672cca5f316a61ad.fq
\ No newline at end of file

data/child_2.fq

+../.git/annex/objects/ZZ/Wp/SHA256E-s141128895--467195f56ce29324b0e2e2d2beb32c88d9955841ca8ef80ecedb3e9c12ce21ba.fq/SHA256E-s141128895--467195f56ce29324b0e2e2d2beb32c88d9955841ca8ef80ecedb3e9c12ce21ba.fq
\ No newline at end of file

data/father.txt

+UD_129077402355: NC_000008.10:136800000_139000000
+

data/father_1.fq

+../.git/annex/objects/Wz/2g/SHA256E-s141128895--b0735baecfbf10641b2990feae2c0b7e98067f148bbc11518650cc9a2ef48283.fq/SHA256E-s141128895--b0735baecfbf10641b2990feae2c0b7e98067f148bbc11518650cc9a2ef48283.fq
\ No newline at end of file

data/father_2.fq

+../.git/annex/objects/80/j7/SHA256E-s141128895--95635532c95b67928cb147753d2b29794f0bd972d1f0e6fc91b20bc8df9ffafc.fq/SHA256E-s141128895--95635532c95b67928cb147753d2b29794f0bd972d1f0e6fc91b20bc8df9ffafc.fq
\ No newline at end of file

data/mother.txt

+father.txt
\ No newline at end of file

data/mother_1.fq

+father_1.fq
\ No newline at end of file

data/mother_2.fq

+father_2.fq
\ No newline at end of file

data/reference.fa

+../.git/annex/objects/6j/fj/SHA256E-s2231520--092a618a228d32cadfa1949fca87dfbb2afed22bc6c317e777cf6fbbd5f6be6b.fa/SHA256E-s2231520--092a618a228d32cadfa1949fca87dfbb2afed22bc6c317e777cf6fbbd5f6be6b.fa
\ No newline at end of file

data/variants.txt

+1660001C>A
+1661001A>T
+1661006T>A
+1662001C>T
+1662005A>G
+1662010A>T
+1663001C>T
+1663005T>G
+1663010A>G
+1663017T>A
+1664001G>C
+1664003T>G
+1664005T>C
+1664007A>C
+1664010A>T
+1664013A>G
+1664017G>T
+1665001del
+1665101_1665102del
+1665201_1665203del
+1665301_1665304del
+1665401_1665406del
+1665501_1665509del
+1665601_1665615del
+1665701_1665735del
+1666002dup
+1666202_1666203dup
+1666402_1666406dup
+1666602_1666611dup
+1666802_1666826dup
+1667002_1667101dup
+1667902_1668601dup
+291001_291002insT
+291201_291202insTA
+291401_291402insTACTC
+291601_291602insTACTCATAGC
+291801_291802insTACTCATAGCTTCCTGTAATCTATT
+292001_292002insTACTCATAGCTTCCTGTAATCTATTTTAGGAGCAATCAAAAATATTTTGAACCATGTCCTCTTCCACTTAGCTTAAGTATGCAATGGAGTATAGTGTCTG
+293001_293002insTACTCATAGCTTCCTGTAATCTATTTTAGGAGCAATCAAAAATATTTTGAACCATGTCCTCTTCCACTTAGCTTAAGTATGCAATGGAGTATAGTGTCTGCCTTTATTAATTCTAATAACTAGTCTCACTGTCCCAAGCCTACTAAATATTTGATTATATGATCCATCTAGTTTCTGTTCCTAGAACCGTGAGAAGTGGAGTGAGAGGAGAGCATTTTGTTTATCATTTAACTCTCAGAGACAGGAATAGGTGTATCCTTGTAAGTGAGAATGAAATCCTGAAGGCAGGGAGTAGGAAATATGGTGTGATTCAGTTCCTCATCTTGAAGAATATCTCCTAAGTTGGCTCTGAAAAGCTGTAGGTGTAATTCTAGCCCCTTGATAATTAGTATTGCCCTATCAGCAGAGGGTGGACATTATGCAAAAAAAAAAAAAAAAAAAAAAAAAACTGGAGAAAATTAAATTGGATGTGGAGTGCCTCCTTTTCTTAAAAAAACAACTTTATTGAGGTGTTATTGATAGACAAAGAACTGCACATATTTCATATATACCATTTGATAAGTTTTAACCTTTGCAAAGACTCATGATACCATTGCCACAACCTAGGTCATCGATATGTCCAACACATCCCTAAGTTTCCTTGTGTTTCTTTGATTTCGTTTTTTGTTTCTGTTTTTATTTTTTGTGGTTCCAACATTTA
+316001C>A
+316002T>G
+316101A>G
+316102_316104del
+317001_317002inv
+317101_317110inv
+317201_317205inv
+317301_317325inv
+317501_317600inv
+319001_319700inv
+320001A>G
+320006del
+320101A>G
+320105dup
+320201T>A
+320205_320206insT